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Found 1 Document (0.712 seconds)

BMRB: 34036

5LQV

Spatial structure of the lentil lipid transfer protein in complex with anionic lysolipid LPPG

Authors

Mineev, K.S., Shenkarev, Z.O., Arseniev, A.S., Melnikova, D.N., Finkina, E.I., Ovchinnikova, T.V.

Assembly

Non-specific lipid-transfer protein 2

Entity

1. Non-specific lipid-transfer protein 2, entity 1 (polymer), 93 monomers, 9291.623 Da Detail

AISCGAVTSD LSPCLTYLTG GPGPSPQCCG GVKKLLAAAN TTPDRQAACN CLKSAAGSIT KLNTNNAAAL PGKCGVNIPY KISTTTNCNT VKF

2. Non-specific lipid-transfer protein 2, entity PGM (non-polymer), 483.553 Da

Total weight

9775.176 Da

Max. entity weight

9291.623 Da

Source organism

Lens culinaris

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 98.5 %, Completeness (bb): 98.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	98.5 % (954 of 969)	99.8 % (495 of 496)	96.6 % (364 of 377)	99.0 % (95 of 96)
Backbone	98.3 % (535 of 544)	99.5 % (187 of 188)	97.4 % (263 of 270)	98.8 % (85 of 86)
Sidechain	98.8 % (503 of 509)	100.0 % (308 of 308)	96.9 % (185 of 191)	100.0 % (10 of 10)
Aromatic	76.9 % (20 of 26)	100.0 % (13 of 13)	53.8 % (7 of 13)
Methyl	100.0 % (110 of 110)	100.0 % (55 of 55)	100.0 % (55 of 55)

1. entity 1

AISCGAVTSD LSPCLTYLTG GPGPSPQCCG GVKKLLAAAN TTPDRQAACN CLKSAAGSIT KLNTNNAAAL PGKCGVNIPY KISTTTNCNT VKF

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 303 K, pH 5.6, Details 0.3 mM [U-99% 13C; U-99% 15N] LTP2, 2 mM LPPG, 20 mM sodium acetate, 0.01 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	LPPG	natural abundance	2 mM
2	LTP2	[U-99% 13C; U-99% 15N]	0.3 mM
3	sodium acetate	natural abundance	20 mM
4	sodium azide	natural abundance	0.01 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.95 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.95 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.03 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.76 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5LQV, Strand ID: A Detail

Release date

2017-06-18

Citation

Ligand Binding Properties of the Lentil Lipid Transfer Protein: Molecular Insight into the Possible Mechanism of Lipid Uptake
Shenkarev, Z.O., Melnikova, D.N., Finkina, E.I., Sukhanov, S.V., Boldyrev, I.A., Gizatullina, A.K., Mineev, K.S., Arseniev, A.S., Ovchinnikova, T.V.
Biochemistry (2017), 56, 1785-1796, PubMed 28266846 , DOI 10.1021/acs.biochem.6b01079 , Abstract

Related entities 1. Non-specific lipid-transfer protein 2, entity 1, : 1 : 2 : 2 : 221 entities Detail

Experiments performed 5 experiments Detail

1 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 303 K, pH 5.6, Details 0.3 mM [U-99% 13C; U-99% 15N] LTP2, 2 mM LPPG, 20 mM sodium acetate, 0.01 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	LPPG	natural abundance	2 mM
2	LTP2	[U-99% 13C; U-99% 15N]	0.3 mM
3	sodium acetate	natural abundance	20 mM
4	sodium azide	natural abundance	0.01 %

2 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LPPG	natural abundance	2 mM
2	LTP2	[U-99% 13C; U-99% 15N]	0.3 mM
3	sodium acetate	natural abundance	20 mM
4	sodium azide	natural abundance	0.01 %

3 3D HNCACB

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LPPG	natural abundance	2 mM
2	LTP2	[U-99% 13C; U-99% 15N]	0.3 mM
3	sodium acetate	natural abundance	20 mM
4	sodium azide	natural abundance	0.01 %

4 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LPPG	natural abundance	2 mM
2	LTP2	[U-99% 13C; U-99% 15N]	0.3 mM
3	sodium acetate	natural abundance	20 mM
4	sodium azide	natural abundance	0.01 %

5 13C-filtered NOESY-HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LPPG	natural abundance	2 mM
2	LTP2	[U-99% 13C; U-99% 15N]	0.3 mM
3	sodium acetate	natural abundance	20 mM
4	sodium azide	natural abundance	0.01 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34036_5lqv.nef
Input source #2: Coordindates	5lqv.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:51:CYS:SG	reduced, CA 54.348, CB 31.059 ppm	oxidized, CA 56.404, CB 35.615 ppm	2.012
A:14:CYS:SG	A:28:CYS:SG	oxidized, CA 53.618, CB 41.577 ppm	oxidized, CA 58.46, CB 36.592 ppm	2.101
A:29:CYS:SG	A:74:CYS:SG	oxidized 53.6%, reduced 46.4%, CA 54.482, CB 32.43 ppm	oxidized 99.1%, reduced 0.9%, CA 51.869, CB 34.891 ppm	1.989
A:49:CYS:SG	A:88:CYS:SG	oxidized, CA 60.154, CB 33.934 ppm	oxidized, CA 54.857, CB 36.004 ppm	1.982

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

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	PGM	1-MYRISTOYL-2-HYDROXY-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)]	None

Sequence alignments

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

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	93	0	0	100.0

Content subtype: combined_34036_5lqv.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_chemical_shifts_1	Warning	965		100.0 (chain: A, length: 93)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1876 (1)	noe	97.8 (chain: A, length: 93)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	24 (1)	undefined	8.6 (chain: A, length: 93)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	Warning	342 (334)	.	100.0 (chain: A, length: 93)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 506
  - ¹³C chemical shifts: 362
  - ¹⁵N chemical shifts: 97
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
3	SER	HG	4.754
16	THR	HG1	4.754
25	SER	HG	6.045
45	ARG	HH21	6.758
45	ARG	HH22	6.758
45	ARG	NH2	72.213
60	THR	HG1	4.748
84	THR	HG1	4.76
85	THR	HG1	5.012
92	LYS	HZ1	7.892
92	LYS	HZ2	7.892
92	LYS	HZ3	7.892

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	496	495	99.8
¹³C chemical shifts	377	362	96.0
¹⁵N chemical shifts	97	96	99.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	188	187	99.5
¹³C chemical shifts	186	177	95.2
¹⁵N chemical shifts	86	85	98.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	308	308	100.0
¹³C chemical shifts	191	185	96.9
¹⁵N chemical shifts	11	11	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	55	55	100.0
¹³C chemical shifts	55	55	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	13	13	100.0
¹³C chemical shifts	13	7	53.8

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 97.8%
- Total number of restraints: 1876
- Weight of restraints: 1.0 (1876)
- Potential type of restraints: upper-bound-parabolic (1876)
- Range of distance target values: 2.47, 5.99 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 8.6%
  - Total number of restraints: 24
  - Weight of restraints: 1.0 (24)
  - Potential type of restraints: upper-bound-parabolic (24)
  - Range of distance target values: 2.0, 3.1 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 100.0%
- Total number of restraints: 334
- Total number of restraints per polymer type: 334
- Weight of restraints: 1.0 (334)
- Potential type of restraints: square-well-parabolic (334)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords LIPID TRANSPORT, STRUCTURE FROM CYANA 3.0, lipid transfer, plant defense peptide lipid transfer protein lens culinaris complex with lipid

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Found 1 Document (0.712 seconds)

BMRB: 34036

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Non-specific lipid-transfer protein 2, entity 1, : 1 : 2 : 2 : 221 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail