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BMRB: 18364

2LRG

NMR structure of the protein YP_001300941.1 from Bacteroides vulgatus

Authors

Dutta, S.K., Serrano, P., Geralt, M., Wuthrich, K., JCSG, J.

Assembly

GS13500A assembly

Entity

1. GS13500A assembly (polymer, Thiol state: all free), 126 monomers, 13474.79 Da Detail

GASDFQTGIH KIVIQQSGDT DSFEVSVSIG GADKGGPAKL YNDKGEYIGD SYSAQIRTAT MSCCTNGNAF FMTCAGSVSS ISEAGKRLHI TVIGYIDDKE VNRLEKEYIT DGNTLIETFS VSTKEI

Formula weight

13474.79 Da

Source organism

Phocaeicola vulgatus

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.2 %, Completeness: 86.5 %, Completeness (bb): 83.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.5 % (1189 of 1374)	92.5 % (650 of 703)	76.0 % (408 of 537)	97.8 % (131 of 134)
Backbone	83.3 % (628 of 754)	97.0 % (257 of 265)	68.1 % (248 of 364)	98.4 % (123 of 125)
Sidechain	91.8 % (672 of 732)	89.7 % (393 of 438)	95.1 % (271 of 285)	88.9 % (8 of 9)
Aromatic	83.7 % (82 of 98)	83.7 % (41 of 49)	83.7 % (41 of 49)
Methyl	97.0 % (130 of 134)	95.5 % (64 of 67)	98.5 % (66 of 67)

1. GS13500A

GASDFQTGIH KIVIQQSGDT DSFEVSVSIG GADKGGPAKL YNDKGEYIGD SYSAQIRTAT MSCCTNGNAF FMTCAGSVSS ISEAGKRLHI TVIGYIDDKE VNRLEKEYIT DGNTLIETFS VSTKEI

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	GS13500A	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		95 mM
5	D2O	[U-99% 2H]		5 mM

LACS Plot; CA

Referencing offset: 2.72 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 2.72 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.06 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2012-04-29

Citation

NMR structure of the protein YP_001300941.1 from Bacteroides vulgatus
Dutta, S.K., Serrano, P., Geralt, M., Wuthrich, K.
Not known

Related entities 1. GS13500A assembly, : 1 : 1 : 5 entities Detail

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	GS13500A	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		95 mM
5	D2O	[U-99% 2H]		5 mM

2 4D APSY-HACANH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	GS13500A	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		95 mM
5	D2O	[U-99% 2H]		5 mM

3 5D APSY-HACACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	GS13500A	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		95 mM
5	D2O	[U-99% 2H]		5 mM

4 5D APSY-CBCACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	GS13500A	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		95 mM
5	D2O	[U-99% 2H]		5 mM

5 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 6.0

#	Name	Isotope labeling	Type	Concentration
1	GS13500A	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		95 mM
5	D2O	[U-99% 2H]		5 mM

6 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	GS13500A	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		95 mM
5	D2O	[U-99% 2H]		5 mM

7 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	GS13500A	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	H2O	natural abundance		95 mM
5	D2O	[U-99% 2H]		5 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18364_2lrg.nef
Input source #2: Coordindates	2lrg.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
GASDFQTGIHKIVIQQSGDTDSFEVSVSIGGADKGGPAKLYNDKGEYIGDSYSAQIRTATMSCCTNGNAFFMTCAGSVSSISEAGKRLHITVIGYIDDKE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GASDFQTGIHKIVIQQSGDTDSFEVSVSIGGADKGGPAKLYNDKGEYIGDSYSAQIRTATMSCCTNGNAFFMTCAGSVSSISEAGKRLHITVIGYIDDKE

-------110-------120------
VNRLEKEYITDGNTLIETFSVSTKEI
||||||||||||||||||||||||||
VNRLEKEYITDGNTLIETFSVSTKEI

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	126	0	0	100.0

Content subtype: combined_18364_2lrg.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1183		98.4 (chain: A, length: 126)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2395 (1)	noe	97.6 (chain: A, length: 126)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 126, Sequence coverage: 98.4%
- Total number of assignments
  - ¹³C chemical shifts: 395
  - ¹H chemical shifts: 658
  - ¹⁵N chemical shifts: 130
- 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: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 126, Sequence coverage: 97.6%
- Total number of restraints: 2395
- Weight of restraints: 1.0 (2395)
- Potential type of restraints: upper-bound-parabolic (2395)
- Range of distance target values: 2.4, 5.5 (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

Keywords Domain of Unknown function (DUF4425)