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BMRB: 18281

2LPX

Solution Structure of Strawberry Allergen Fra a 1e

Authors

Seutter von Loetzen, C., Hartl-Spiegelhauer, O., Schweimer, K., Schwab, W., Roesch, P.

Assembly

Strawberry

Entity

1. Strawberry (polymer, Thiol state: all free), 170 monomers, 18976.11 Da Detail

MGVYTYENEF TSDIPAPKLF KAFVLDADNL IPKIAPQAVK CAEILEGDGG PGTIKKITFG EGSHYGYVKH KIHSIDKVNH TYSYSLIEGD ALSENIEKID YETKLVSAPH GGTIIKTTSK YHTKGDVEIK EEHVKAGKEK AAHLFKLIEG YLKDHPSEYN GSRSHHHHHH

Formula weight

18976.11 Da

Source organism

Fragaria x ananassa

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 90.6 %, Completeness: 79.1 %, Completeness (bb): 85.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	79.1 % (1566 of 1979)	78.5 % (805 of 1025)	78.2 % (614 of 785)	87.0 % (147 of 169)
Backbone	85.6 % (861 of 1006)	85.9 % (299 of 348)	84.6 % (419 of 495)	87.7 % (143 of 163)
Sidechain	74.5 % (840 of 1128)	74.7 % (506 of 677)	74.2 % (330 of 445)	66.7 % (4 of 6)
Aromatic	24.7 % (47 of 190)	38.9 % (37 of 95)	10.5 % (10 of 95)
Methyl	97.7 % (170 of 174)	96.6 % (84 of 87)	98.9 % (86 of 87)

1. entity

MGVYTYENEF TSDIPAPKLF KAFVLDADNL IPKIAPQAVK CAEILEGDGG PGTIKKITFG EGSHYGYVKH KIHSIDKVNH TYSYSLIEGD ALSENIEKID YETKLVSAPH GGTIIKTTSK YHTKGDVEIK EEHVKAGKEK AAHLFKLIEG YLKDHPSEYN GSRSHHHHHH

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Strawberry	[U-99% 13C; U-99% 15N]		700 uM
2	sodium chloride	natural abundance		150 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

Protein Blocks Logo

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

Release date

2012-03-21

Citation

Solution structure of the strawberry allergen Fra a 1
Seutter von Loetzen, C., Schweimer, K., Schwab, W., Rosch, P., Hartl-Spiegelhauer, O.
Biosci. Rep. (2012), 32, 567-575, PubMed 22913709 , DOI 10.1042/BSR20120058 , Abstract

Related entities 1. Strawberry, : 1 : 3 : 197 entities Detail

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Strawberry	[U-99% 13C; U-99% 15N]		700 uM
2	sodium chloride	natural abundance		150 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Strawberry	[U-99% 13C; U-99% 15N]		700 uM
2	sodium chloride	natural abundance		150 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Strawberry	[U-99% 13C; U-99% 15N]		700 uM
2	sodium chloride	natural abundance		150 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

4 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Strawberry	[U-99% 13C; U-99% 15N]		700 uM
2	sodium chloride	natural abundance		150 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

5 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Strawberry	[U-99% 13C; U-99% 15N]		700 uM
2	sodium chloride	natural abundance		150 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

6 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Strawberry	[U-99% 13C; U-99% 15N]		700 uM
2	sodium chloride	natural abundance		150 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

7 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Strawberry	[U-99% 13C; U-99% 15N]		700 uM
2	sodium chloride	natural abundance		150 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

8 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Strawberry	[U-99% 13C; U-99% 15N]		700 uM
2	sodium chloride	natural abundance		150 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

9 3D C(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Strawberry	[U-99% 13C; U-99% 15N]		700 uM
2	sodium chloride	natural abundance		150 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Strawberry	[U-99% 13C; U-99% 15N]		700 uM
2	sodium chloride	natural abundance		150 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

11 3D CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Strawberry	[U-99% 13C; U-99% 15N]		700 uM
2	sodium chloride	natural abundance		150 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

12 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Strawberry	[U-99% 13C; U-99% 15N]		700 uM
2	sodium chloride	natural abundance		150 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

13 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Strawberry	[U-99% 13C; U-99% 15N]		700 uM
2	sodium chloride	natural abundance		150 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

14 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Strawberry	[U-99% 13C; U-99% 15N]		700 uM
2	sodium chloride	natural abundance		150 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18281_2lpx.nef
Input source #2: Coordindates	2lpx.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

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-------100
MGVYTYENEFTSDIPAPKLFKAFVLDADNLIPKIAPQAVKCAEILEGDGGPGTIKKITFGEGSHYGYVKHKIHSIDKVNHTYSYSLIEGDALSENIEKID
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGVYTYENEFTSDIPAPKLFKAFVLDADNLIPKIAPQAVKCAEILEGDGGPGTIKKITFGEGSHYGYVKHKIHSIDKVNHTYSYSLIEGDALSENIEKID

-------110-------120-------130-------140-------150-------160-------170
YETKLVSAPHGGTIIKTTSKYHTKGDVEIKEEHVKAGKEKAAHLFKLIEGYLKDHPSEYNGSRSHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
YETKLVSAPHGGTIIKTTSKYHTKGDVEIKEEHVKAGKEKAAHLFKLIEGYLKDHPSEYNGSRSHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	170	0	0	100.0

Content subtype: combined_18281_2lpx.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1561		89.4 (chain: A, length: 170)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1588 (1)	noe	87.1 (chain: A, length: 170)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	6 (1)	noe	1.2 (chain: A, length: 170)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	122 (1)	hbond	48.2 (chain: A, length: 170)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	209 (209)	.	79.4 (chain: A, length: 170)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 170, Sequence coverage: 89.4%
- Total number of assignments
  - ¹H chemical shifts: 808
  - ¹³C chemical shifts: 609
  - ¹⁵N chemical shifts: 144
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 170, Sequence coverage: 87.1%
- Total number of restraints: 1587
- Weight of restraints: 1.0 (1587)
- Potential type of restraints: square-well-parabolic (1587)
- Range of distance target values: 1.5, 3.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 170, Sequence coverage: 1.2%
  - Total number of restraints: 6
  - Weight of restraints: 1.0 (6)
  - Potential type of restraints: square-well-parabolic (6)
  - Range of distance target values: 3.0, 3.0 (Å)
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_4
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 170, Sequence coverage: 48.2%
    - Total number of restraints: 122
    - Weight of restraints: 1.0 (122)
    - Potential type of restraints: square-well-parabolic (122)
    - Range of distance target values: 1.15, 1.65 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 170, Sequence coverage: 79.4%
- Total number of restraints: 209
- Total number of restraints per polymer type: 209
- Weight of restraints: 1.0 (209)
- Potential type of restraints: square-well-parabolic (209)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords allergen, Fra a 1e, strawberry