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BMRB: 19453

2MCT

NMR structure of the protein ZP_02042476.1 from Ruminococcus gnavus

Authors

Martin, B.T., Serrano, P., Geralt, M., Dutta, S., Wuthrich, K.

Assembly

SP17945A

Entity

1. SP17945A (polymer, Thiol state: all free), 100 monomers, 11558.68 Da Detail

PILPKAENVD SICIDFTNSI QKIYDDSESI QKILSEIATG KRTEKQSIQD YPSAEEYGTI NIENNGGMTT MFYYEENGKY YIECPYKGIY EIENNFEDMI

Formula weight

11558.68 Da

Source organism

[Ruminococcus] gnavus ATCC 29149

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 87.7 %, Completeness (bb): 84.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.7 % (1040 of 1186)	96.3 % (597 of 620)	73.1 % (335 of 458)	100.0 % (108 of 108)
Backbone	84.3 % (499 of 592)	99.0 % (200 of 202)	69.0 % (203 of 294)	100.0 % (96 of 96)
Sidechain	92.3 % (635 of 688)	95.0 % (397 of 418)	87.6 % (226 of 258)	100.0 % (12 of 12)
Aromatic	67.6 % (69 of 102)	88.2 % (45 of 51)	47.1 % (24 of 51)
Methyl	96.7 % (87 of 90)	95.6 % (43 of 45)	97.8 % (44 of 45)

1. entity

PILPKAENVD SICIDFTNSI QKIYDDSESI QKILSEIATG KRTEKQSIQD YPSAEEYGTI NIENNGGMTT MFYYEENGKY YIECPYKGIY EIENNFEDMI

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	D2O	natural abundance		5 %
6	H2O	natural abundance		95 %

LACS Plot; CA

Referencing offset: -0.04 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.04 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.05 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2013-11-10

Citation

NMR structure of the protein ZP_02042476.1 from Ruminococcus gnavus
Martin, B.T., Wuthrich, K., Serrano, P., Geralt, M., Dutta, S.K.
Not known

Related entities 1. SP17945A, : 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	D2O	natural abundance		5 %
6	H2O	natural abundance		95 %

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	D2O	natural abundance		5 %
6	H2O	natural abundance		95 %

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	D2O	natural abundance		5 %
6	H2O	natural abundance		95 %

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	D2O	natural abundance		5 %
6	H2O	natural abundance		95 %

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	D2O	natural abundance		5 %
6	H2O	natural abundance		95 %

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	D2O	natural abundance		5 %
6	H2O	natural abundance		95 %

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	D2O	natural abundance		5 %
6	H2O	natural abundance		95 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19453_2mct.nef
Input source #2: Coordindates	2mct.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
GSPILPKAENVDSICIDFTNSIQKIYDDSESIQKILSEIATGKRTEKQSIQDYPSAEEYGTINIENNGGMTTMFYYEENGKYYIECPYKGIYEIENNFED
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSPILPKAENVDSICIDFTNSIQKIYDDSESIQKILSEIATGKRTEKQSIQDYPSAEEYGTINIENNGGMTTMFYYEENGKYYIECPYKGIYEIENNFED

--
MI
||
MI

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	102	0	0	100.0

Content subtype: combined_19453_2mct.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1033		98.0 (chain: A, length: 102)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2095 (1)	noe	98.0 (chain: A, length: 102)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 98.0%
- Total number of assignments
  - ¹H chemical shifts: 600
  - ¹³C chemical shifts: 325
  - ¹⁵N chemical shifts: 108
- 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: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 98.0%
- Total number of restraints: 2095
- Weight of restraints: 1.0 (2095)
- Potential type of restraints: upper-bound-parabolic (2095)
- 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