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BMRB: 25830

2N81

Solution Structure of Lipid Transfer Protein From Pea Pisum Sativum

Authors

Paramonov, A.S., Rumynskiy, E.I., Bogdanov, I.V., Ovchinnikova, T.V., Shenkarev, Z.O.

Assembly

Lipid Transfer Protein From Pea Pisum Sativum

Entity

1. Lipid Transfer Protein From Pea Pisum Sativum (polymer), 95 monomers, 9537.928 Da Detail

ALSCGTVSAD LAPCVTYLQA PNNASPPPPC CAGVKKLLAA ATTTPDRQAA CNCLKSAAGS IPKLNTNNAA ALPGKCGVSI PYKISTSTNC NTVRF

Formula weight

9537.928 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 98.5 %, Completeness (bb): 98.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	98.5 % (979 of 994)	99.4 % (507 of 510)	96.9 % (377 of 389)	100.0 % (95 of 95)
Backbone	98.5 % (542 of 550)	98.9 % (183 of 185)	97.9 % (274 of 280)	100.0 % (85 of 85)
Sidechain	98.7 % (527 of 534)	99.7 % (324 of 325)	97.0 % (193 of 199)	100.0 % (10 of 10)
Aromatic	76.9 % (20 of 26)	100.0 % (13 of 13)	53.8 % (7 of 13)
Methyl	99.1 % (113 of 114)	98.2 % (56 of 57)	100.0 % (57 of 57)

1. Ps-LTP1

ALSCGTVSAD LAPCVTYLQA PNNASPPPPC CAGVKKLLAA ATTTPDRQAA CNCLKSAAGS IPKLNTNNAA ALPGKCGVSI PYKISTSTNC NTVRF

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	PS-LTP1	[U-98% 13C; U-98% 15N]		1 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: 2.91 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 2.91 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 2.72 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2N81, Strand ID: A Detail

Release date

2016-05-22

Citation

A novel lipid transfer protein from the pea Pisum sativum: isolation, recombinant expression, solution structure, antifungal activity, lipid binding, and allergenic properties
Bogdanov, I.V., Shenkarev, Z.O., Paramonov, A.S., Rumynskiy, E.I., Finkina, E.I., Melnikova, D.N., Arseniev, A.S., Ovchinnikova, T.V.
BMC Plant Biol. (2016), 16, 107-107, PubMed 27137920 , DOI 10.1186/s12870-016-0792-6 , Abstract

Related entities 1. Lipid Transfer Protein From Pea Pisum Sativum, : 1 : 1 : 215 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	PS-LTP1	[U-98% 13C; U-98% 15N]		1 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	PS-LTP1	[U-98% 13C; U-98% 15N]		1 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

3 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	PS-LTP1	[U-98% 13C; U-98% 15N]		1 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

4 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	PS-LTP1	[U-98% 13C; U-98% 15N]		1 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

5 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	PS-LTP1	[U-98% 13C; U-98% 15N]		1 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

6 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	PS-LTP1	[U-98% 13C; U-98% 15N]		1 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

7 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	PS-LTP1	[U-98% 13C; U-98% 15N]		1 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

8 3D 1H-15N TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	PS-LTP1	[U-98% 13C; U-98% 15N]		1 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	PS-LTP1	[U-98% 13C; U-98% 15N]		1 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

10 3D HN(CO)CA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	PS-LTP1	[U-98% 13C; U-98% 15N]		1 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

NMR combined restraints 12 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25830_2n81.nef
Input source #2: Coordindates	2n81.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:4:CYS:SG	A:53:CYS:SG	reduced, CA 52.166, CB 30.372 ppm	reduced, CA 53.637, CB 34.302 ppm	2.0
A:14:CYS:SG	A:30:CYS:SG	oxidized, CA 51.481, CB 39.508 ppm	oxidized, CA 55.585, CB 34.602 ppm	1.952
A:31:CYS:SG	A:76:CYS:SG	reduced, CA 51.858, CB 29.979 ppm	reduced, CA 49.73, CB 32.817 ppm	1.958
A:51:CYS:SG	A:90:CYS:SG	oxidized, CA 57.66, CB 34.278 ppm	oxidized, CA 54.158, CB 36.687 ppm	2.094

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-----
ALSCGTVSADLAPCVTYLQAPNNASPPPPCCAGVKKLLAAATTTPDRQAACNCLKSAAGSIPKLNTNNAAALPGKCGVSIPYKISTSTNCNTVRF
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ALSCGTVSADLAPCVTYLQAPNNASPPPPCCAGVKKLLAAATTTPDRQAACNCLKSAAGSIPKLNTNNAAALPGKCGVSIPYKISTSTNCNTVRF

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	95	0	0	100.0

Content subtype: combined_25830_2n81.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	984		100.0 (chain: A, length: 95)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	28 (1)	undefined	4.2 (chain: A, length: 95)
2	Distance restraints	DYANA/DIANA_distance_constraints_6	Warning	26 (1)	noe	21.1 (chain: A, length: 95)
3	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	567 (1)	noe	100.0 (chain: A, length: 95)
4	Distance restraints	DYANA/DIANA_distance_constraints_10	Warning	12 (1)	undefined	8.4 (chain: A, length: 95)
5	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	5 (1)	undefined	3.2 (chain: A, length: 95)
6	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	4 (1)	noe	2.1 (chain: A, length: 95)
7	Distance restraints	DYANA/DIANA_distance_constraints_8	Warning	40 (1)	undefined	12.6 (chain: A, length: 95)
8	Distance restraints	DYANA/DIANA_distance_constraints_7	OK	104 (1)	hbond	72.6 (chain: A, length: 95)
9	Distance restraints	DYANA/DIANA_distance_constraints_9	Warning	104 (1)	hbond	72.6 (chain: A, length: 95)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_11	Warning	1478 (1460)	.	97.9 (chain: A, length: 95)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 509
  - ¹³C chemical shifts: 379
  - ¹⁵N chemical shifts: 96
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 4.2%
- Total number of restraints: 28
- Weight of restraints: 1.0 (28)
- Potential type of restraints: upper-bound-parabolic (28)
- Range of distance target values: 1.51, 2.4 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_6
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 21.1%
  - Total number of restraints: 26
  - Weight of restraints: 1.0 (26)
  - Potential type of restraints: upper-bound-parabolic (26)
  - Range of distance target values: 0.0, 3.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_2
    - Status: OK
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 100.0%
    - Total number of restraints: 567
    - Weight of restraints: 1.0 (567)
    - Potential type of restraints: upper-bound-parabolic (567)
    - Range of distance target values: 2.4, 5.57 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map
    - Saveframe: DYANA/DIANA_distance_constraints_10
      - Status: Warning
      - Experiment type: undefined
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 8.4%
      - Total number of restraints: 12
        Long range restraints, | i - j | >= 5 : 8
        Total disulfide bond restraints: 4
      - Weight of restraints: 1.0 (12)
        Long range restraints, | i - j | >= 5 : 1.0 (8)
        Total disulfide bond restraints: 1.0 (4)
      - Potential type of restraints: upper-bound-parabolic (12)
        Long range restraints, | i - j | >= 5 : upper-bound-parabolic (8)
        Total disulfide bond restraints: upper-bound-parabolic (4)
      - Range of distance target values: 2.0, 3.0 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map
      - Saveframe: DYANA/DIANA_distance_constraints_5
        Status: Warning
        Experiment type: undefined
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 3.2%
        Total number of restraints: 5
        Sequential restraints, | i - j | = 1 : 3
        Backbone-side chain: 3
        Medium range restraints, 1 < | i - j | < 5 : 2
        Backbone-side chain: 2
        Weight of restraints: 1.0 (5)
        Sequential restraints, | i - j | = 1 : 1.0 (3)
        Backbone-side chain: 1.0 (3)
        Medium range restraints, 1 < | i - j | < 5 : 1.0 (2)
        Backbone-side chain: 1.0 (2)
        Potential type of restraints: upper-bound-parabolic (5)
        Sequential restraints, | i - j | = 1 : upper-bound-parabolic (3)
        Backbone-side chain: upper-bound-parabolic (3)
        Medium range restraints, 1 < | i - j | < 5 : upper-bound-parabolic (2)
        Backbone-side chain: upper-bound-parabolic (2)
        Range of distance target values: 0.0, 3.7 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Saveframe: DYANA/DIANA_distance_constraints_4
        Status: Warning
        Experiment type: noe
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 2.1%
        Total number of restraints: 4
        Sequential restraints, | i - j | = 1 : 4
        Backbone-side chain: 2
        Side chain-side chain: 2
        Weight of restraints: 1.0 (4)
        Sequential restraints, | i - j | = 1 : 1.0 (4)
        Backbone-side chain: 1.0 (2)
        Side chain-side chain: 1.0 (2)
        Potential type of restraints: upper-bound-parabolic (4)
        Sequential restraints, | i - j | = 1 : upper-bound-parabolic (4)
        Backbone-side chain: upper-bound-parabolic (2)
        Side chain-side chain: upper-bound-parabolic (2)
        Range of distance target values: 0.0, 3.9 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Saveframe: DYANA/DIANA_distance_constraints_8
        Status: Warning
        Experiment type: undefined
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 12.6%
        Total number of restraints: 40
        Intra-residue restraints, i = j : 28
        Long range restraints, | i - j | >= 5 : 8
        Total disulfide bond restraints: 4
        Weight of restraints: 1.0 (40)
        Intra-residue restraints, i = j : 1.0 (28)
        Long range restraints, | i - j | >= 5 : 1.0 (8)
        Total disulfide bond restraints: 1.0 (4)
        Potential type of restraints: upper-bound-parabolic (40)
        Intra-residue restraints, i = j : upper-bound-parabolic (28)
        Long range restraints, | i - j | >= 5 : upper-bound-parabolic (8)
        Total disulfide bond restraints: upper-bound-parabolic (4)
        Range of distance target values: 1.49, 3.1 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Saveframe: DYANA/DIANA_distance_constraints_7
        Status: OK
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 72.6%
        --------10--------20--------30--------40--------50--------60--------70--------80--------90----- ALSCGTVSADLAPCVTYLQAPNNASPPPPCCAGVKKLLAAATTTPDRQAACNCLKSAAGSIPKLNTNNAAALPGKCGVSIPYKISTSTNCNTVRF || |||| || |||||||| | || ||||||||||| ||||||||||| ||||||| ||||||||||||||| | ||| || ..SC.TVSA.LA.CVTYLQAP..A..PP.CCAGVKKLLAA..TTPDRQAACNC.KSAAGSI..LNTNNAAALPGKCGV......S..TNC.TV --------10--------20--------30--------40--------50--------60--------70--------80--------90---
        Total number of restraints: 104
        Total hydrogen bond restraints: 104
        O...H-x: 50
        O...h-N: 50
        Long range: 4
        O...H-x: 2
        O...h-N: 2
        Weight of restraints: 1.0 (104)
        Total hydrogen bond restraints: 1.0 (104)
        O...H-x: 1.0 (50)
        O...h-N: 1.0 (50)
        Long range: 1.0 (4)
        O...H-x: 1.0 (2)
        O...h-N: 1.0 (2)
        Potential type of restraints: upper-bound-parabolic (104)
        Total hydrogen bond restraints: upper-bound-parabolic (104)
        O...H-x: upper-bound-parabolic (50)
        O...h-N: upper-bound-parabolic (50)
        Long range: upper-bound-parabolic (4)
        O...H-x: upper-bound-parabolic (2)
        O...h-N: upper-bound-parabolic (2)
        Range of distance target values: 2.3, 3.5 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A
        Saveframe: DYANA/DIANA_distance_constraints_9
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 72.6%
        --------10--------20--------30--------40--------50--------60--------70--------80--------90----- ALSCGTVSADLAPCVTYLQAPNNASPPPPCCAGVKKLLAAATTTPDRQAACNCLKSAAGSIPKLNTNNAAALPGKCGVSIPYKISTSTNCNTVRF || |||| || |||||||| | || ||||||||||| ||||||||||| ||||||| ||||||||||||||| | ||| || ..SC.TVSA.LA.CVTYLQAP..A..PP.CCAGVKKLLAA..TTPDRQAACNC.KSAAGSI..LNTNNAAALPGKCGV......S..TNC.TV --------10--------20--------30--------40--------50--------60--------70--------80--------90---
        Total number of restraints: 104
        Total hydrogen bond restraints: 104
        O...H-x (too close!): 50
        O...h-N (too close!): 50
        Long range: 4
        O...H-x (too close!): 2
        O...h-N (too close!): 2
        Weight of restraints: 1.0 (104)
        Total hydrogen bond restraints: 1.0 (104)
        O...H-x (too close!): 1.0 (50)
        O...h-N (too close!): 1.0 (50)
        Long range: 1.0 (4)
        O...H-x (too close!): 1.0 (2)
        O...h-N (too close!): 1.0 (2)
        Potential type of restraints: upper-bound-parabolic (104)
        Total hydrogen bond restraints: upper-bound-parabolic (104)
        O...H-x (too close!): upper-bound-parabolic (50)
        O...h-N (too close!): upper-bound-parabolic (50)
        Long range: upper-bound-parabolic (4)
        O...H-x (too close!): upper-bound-parabolic (2)
        O...h-N (too close!): upper-bound-parabolic (2)
        Range of distance target values: 1.8, 2.7 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_11
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 97.9%
- Total number of restraints: 1460
- Total number of restraints per polymer type: 1460
- Weight of restraints: 1.0 (1460)
- Potential type of restraints: square-well-parabolic (1460)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords allergen, antimicrobial activity, lipid binding, lipid transfer protein, ltp