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BMRB: 18107

2LM9

The NMR structure of a major allergen from dust mite

Authors

Tan, K., Mok, Y.

Assembly

a major allergen from dust mite

Entity

1. a major allergen from dust mite (polymer, Thiol state: not present), 96 monomers, 11189.48 Da Detail

NTATQRFHEI EKFLLHITHE VDDLEKTGNK DEKARLLREL TVSEAFIEGS RGYFQRELKR TDLDLLEKFN FEAALATGDL LLKDLKALQK RVQDSE

Formula weight

11189.48 Da

Source organism

Blomia tropicalis

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 79.9 %, Completeness (bb): 82.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	79.9 % (928 of 1162)	86.3 % (525 of 608)	68.3 % (308 of 451)	92.2 % (95 of 103)
Backbone	82.6 % (476 of 576)	95.9 % (188 of 196)	68.0 % (193 of 284)	99.0 % (95 of 96)
Sidechain	79.6 % (540 of 678)	81.8 % (337 of 412)	78.4 % (203 of 259)	0.0 % (0 of 7)
Aromatic	0.0 % (0 of 80)	0.0 % (0 of 40)	0.0 % (0 of 40)
Methyl	95.7 % (111 of 116)	100.0 % (58 of 58)	91.4 % (53 of 58)

1. entity

NTATQRFHEI EKFLLHITHE VDDLEKTGNK DEKARLLREL TVSEAFIEGS RGYFQRELKR TDLDLLEKFN FEAALATGDL LLKDLKALQK RVQDSE

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		0.8 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	entity	natural abundance		0.8 ug/mL

Protein Blocks Logo

Calculated from 20 models in PDB: 2LM9, Strand ID: A Detail

Release date

2012-08-20

Citation

NMR structure and IgE epitopes of Blo t 21, a major dust mite allergen from Blomia tropicalis
Tan, K., Ong, T., Gao, Y., Tiong, Y., Wong, K., Chew, F., Mok, Y.
J. Biol. Chem. (2012), 287, 34776-34785, PubMed 22887997 , DOI 10.1074/jbc.M112.348730 , Abstract

Related entities 1. a major allergen from dust mite, : 1 : 8 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		0.8 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	entity	natural abundance		0.8 ug/mL

2 2D DQF-COSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		0.8 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	entity	natural abundance		0.8 ug/mL

3 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		0.8 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	entity	natural abundance		0.8 ug/mL

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		0.8 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	entity	natural abundance		0.8 ug/mL

5 3D C(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		0.8 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	entity	natural abundance		0.8 ug/mL

6 3D H(CCO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		0.8 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	entity	natural abundance		0.8 ug/mL

7 2D 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		0.8 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	entity	natural abundance		0.8 ug/mL

8 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		0.8 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	entity	natural abundance		0.8 ug/mL

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		0.8 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	entity	natural abundance		0.8 ug/mL

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		0.8 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	entity	natural abundance		0.8 ug/mL

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18107_2lm9.nef
Input source #2: Coordindates	2lm9.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

--20-------30--------40--------50--------60--------70--------80--------90-------100-------110---
NTATQRFHEIEKFLLHITHEVDDLEKTGNKDEKARLLRELTVSEAFIEGSRGYFQRELKRTDLDLLEKFNFEAALATGDLLLKDLKALQKRVQDSE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NTATQRFHEIEKFLLHITHEVDDLEKTGNKDEKARLLRELTVSEAFIEGSRGYFQRELKRTDLDLLEKFNFEAALATGDLLLKDLKALQKRVQDSE
--------10--------20--------30--------40--------50--------60--------70--------80--------90------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	96	0	0	100.0

Content subtype: combined_18107_2lm9.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	914		100.0 (chain: A, length: 96)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	2053 (1)	noe	99.0 (chain: A, length: 96)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	138 (138)	.	96.9 (chain: A, length: 96)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 529
  - ¹⁵N chemical shifts: 94
  - ¹³C chemical shifts: 291
- Completeness of assignments
  - Entity_assemble_ID: A
- 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_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 99.0%
- Total number of restraints: 2052
- Weight of restraints: 1.0 (2052)
- Potential type of restraints: square-well-parabolic (2052)
- Range of distance target values: 2.35, 5.8 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 96.9%
- Total number of restraints: 138
- Total number of restraints per polymer type: 138
- Weight of restraints: 1.0 (138)
- Potential type of restraints: square-well-parabolic (138)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords allergen, dust mite