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BMRB: 19433

2MCA

NMR structure of the protein YP_002937094.1 from Eubacterium rectale

Authors

Proudfoot, A., Serrano, P., Geralt, M., Dutta, S., Wuthrich, K.

Assembly

YP 002937094.1

Entity

1. YP 002937094.1 (polymer, Thiol state: not present), 103 monomers, 11346.32 Da Detail

GAQDGKETTT IRLINQTYFN VKNIKVTWND GKEQTVNTLG SHDSIDFSSD AGSVYKMDVT GTTQSGEKFT GHFKGLVGKD TRVFIELDEN ADVQVFIPQG EID

Formula weight

11346.32 Da

Source organism

[Eubacterium] rectale

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.0 %, Completeness: 88.9 %, Completeness (bb): 83.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.9 % (1037 of 1167)	95.5 % (573 of 600)	77.7 % (351 of 452)	98.3 % (113 of 115)
Backbone	83.4 % (514 of 616)	96.8 % (209 of 216)	68.5 % (204 of 298)	99.0 % (101 of 102)
Sidechain	95.5 % (614 of 643)	94.8 % (364 of 384)	96.7 % (238 of 246)	92.3 % (12 of 13)
Aromatic	84.4 % (81 of 96)	83.3 % (40 of 48)	85.1 % (40 of 47)	100.0 % (1 of 1)
Methyl	100.0 % (110 of 110)	100.0 % (55 of 55)	100.0 % (55 of 55)

1. entity

GAQDGKETTT IRLINQTYFN VKNIKVTWND GKEQTVNTLG SHDSIDFSSD AGSVYKMDVT GTTQSGEKFT GHFKGLVGKD TRVFIELDEN ADVQVFIPQG EID

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	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	H20	natural abundance		95 %
6	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: 2.79 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 2.79 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.03 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2013-09-02

Citation

NMR structure of the protein YP_002937094.1 from Eubacterium rectale
Proudfoot, A., Wuthrich, K., Serrano, P., Geralt, M., Dutta, S.K.
Not known

Related entities 1. YP 002937094.1, : 1 : 2 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	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	H20	natural abundance		95 %
6	D2O	natural abundance		5 %

2 3D 1H-13C NOESY aliphatic

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	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	H20	natural abundance		95 %
6	D2O	natural abundance		5 %

3 3D 1H-13C NOESY aromatic

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	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	H20	natural abundance		95 %
6	D2O	natural abundance		5 %

4 3D 1H-15N NOESY

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	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	H20	natural abundance		95 %
6	D2O	natural abundance		5 %

5 APSY 4D-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	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	H20	natural abundance		95 %
6	D2O	natural abundance		5 %

6 APSY 5D-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	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	H20	natural abundance		95 %
6	D2O	natural abundance		5 %

7 APSY 5D-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	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	H20	natural abundance		95 %
6	D2O	natural abundance		5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19433_2mca.nef
Input source #2: Coordindates	2mca.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
GAQDGKETTTIRLINQTYFNVKNIKVTWNDGKEQTVNTLGSHDSIDFSSDAGSVYKMDVTGTTQSGEKFTGHFKGLVGKDTRVFIELDENADVQVFIPQG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAQDGKETTTIRLINQTYFNVKNIKVTWNDGKEQTVNTLGSHDSIDFSSDAGSVYKMDVTGTTQSGEKFTGHFKGLVGKDTRVFIELDENADVQVFIPQG

---
EID
|||
EID

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	103	0	0	100.0

Content subtype: combined_19433_2mca.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1034		99.0 (chain: A, length: 103)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2486 (1)	noe	99.0 (chain: A, length: 103)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 103, Sequence coverage: 99.0%
- Total number of assignments
  - ¹H chemical shifts: 582
  - ¹³C chemical shifts: 340
  - ¹⁵N chemical shifts: 112
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: 103, Sequence coverage: 99.0%
- Total number of restraints: 2486
- Weight of restraints: 1.0 (2486)
- Potential type of restraints: upper-bound-parabolic (2486)
- 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 Unknown Function