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BMRB: 25294

2MW1

NMR structure of the protein NP_809137.1 from Bacteroides thetaiotaomicron

Authors

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

Assembly

NP 809137.1 monomer

Entity

1. NP 809137.1 monomer (polymer, Thiol state: all free), 118 monomers, 13173.56 Da Detail

GCELSDPDGL ADPMKWSKVP SGLKNGELKV EAEGGSSLFA CKNYKSFWIS SVKEEGKFKE NTSYKEFDGG WYLVKIEDNE LKVIINRNET NASRSFTVCV EAGNAFDEFK FVQDAAKQ

Formula weight

13173.56 Da

Source organism

Bacteroides thetaiotaomicron

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.6 %, Completeness: 87.3 %, Completeness (bb): 83.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.3 % (1205 of 1381)	93.2 % (672 of 721)	76.9 % (409 of 532)	96.9 % (124 of 128)
Backbone	83.0 % (583 of 702)	93.8 % (228 of 243)	70.9 % (244 of 344)	96.5 % (111 of 115)
Sidechain	92.4 % (727 of 787)	92.9 % (444 of 478)	91.2 % (270 of 296)	100.0 % (13 of 13)
Aromatic	87.9 % (123 of 140)	91.4 % (64 of 70)	83.6 % (56 of 67)	100.0 % (3 of 3)
Methyl	93.9 % (92 of 98)	93.9 % (46 of 49)	93.9 % (46 of 49)

1. entity

GCELSDPDGL ADPMKWSKVP SGLKNGELKV EAEGGSSLFA CKNYKSFWIS SVKEEGKFKE NTSYKEFDGG WYLVKIEDNE LKVIINRNET NASRSFTVCV EAGNAFDEFK FVQDAAKQ

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	DTT	[U-99% 2H]		5 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: 2.57 ppm, Outliers: 3 Detail

LACS Plot; CB

Referencing offset: 2.57 ppm, Outliers: 3 Detail

LACS Plot; HA

Referencing offset: 0.02 ppm, Outliers: 6 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MW1, Strand ID: A Detail

Release date

2014-11-09

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. NP 809137.1 monomer, : 1 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	DTT	[U-99% 2H]		5 mM
6	H2O	natural abundance		95 %
7	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	DTT	[U-99% 2H]		5 mM
6	H2O	natural abundance		95 %
7	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	DTT	[U-99% 2H]		5 mM
6	H2O	natural abundance		95 %
7	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	DTT	[U-99% 2H]		5 mM
6	H2O	natural abundance		95 %
7	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	DTT	[U-99% 2H]		5 mM
6	H2O	natural abundance		95 %
7	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	DTT	[U-99% 2H]		5 mM
6	H2O	natural abundance		95 %
7	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	DTT	[U-99% 2H]		5 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25294_2mw1.nef
Input source #2: Coordindates	2mw1.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
GCELSDPDGLADPMKWSKVPSGLKNGELKVEAEGGSSLFACKNYKSFWISSVKEEGKFKENTSYKEFDGGWYLVKIEDNELKVIINRNETNASRSFTVCV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GCELSDPDGLADPMKWSKVPSGLKNGELKVEAEGGSSLFACKNYKSFWISSVKEEGKFKENTSYKEFDGGWYLVKIEDNELKVIINRNETNASRSFTVCV

-------110--------
EAGNAFDEFKFVQDAAKQ
||||||||||||||||||
EAGNAFDEFKFVQDAAKQ

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	118	0	0	100.0

Content subtype: combined_25294_2mw1.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1176		96.6 (chain: A, length: 118)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	2400 (1)	noe	96.6 (chain: A, length: 118)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 118, Sequence coverage: 96.6%
- Total number of assignments
  - ¹H chemical shifts: 668
  - ¹³C chemical shifts: 384
  - ¹⁵N chemical shifts: 124
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 118, Sequence coverage: 96.6%
- Total number of restraints: 2400
- Weight of restraints: 1.0 (2400)
- Potential type of restraints: upper-bound-parabolic (2400)
- 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