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BMRB: 19431

2MC8

NMR structure of hypothetical protein RUMGNA_01855 from Ruminococcus gnavus ATCC 29149

Authors

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

Assembly

hypothetical protein

Entity

1. hypothetical protein (polymer, Thiol state: all free), 114 monomers, 13264.74 Da Detail

GEILKELPEG FDKETVRKQA MEDIEIAQSK DYESWKSRFT KDLQSSLTEE SYDSYLKILE KQGEFKEFGK CTYLGQIKDN KKYGGVIIVV KYEEGNVNYS LAYDEDMNLV SFTM

Formula weight

13264.74 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: 89.2 %, Completeness (bb): 84.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.2 % (1235 of 1384)	95.3 % (692 of 726)	78.7 % (421 of 535)	99.2 % (122 of 123)
Backbone	84.5 % (576 of 682)	97.0 % (228 of 235)	70.7 % (236 of 334)	99.1 % (112 of 113)
Sidechain	94.4 % (763 of 808)	94.5 % (464 of 491)	94.1 % (289 of 307)	100.0 % (10 of 10)
Aromatic	83.3 % (105 of 126)	87.3 % (55 of 63)	79.0 % (49 of 62)	100.0 % (1 of 1)
Methyl	98.1 % (102 of 104)	98.1 % (51 of 52)	98.1 % (51 of 52)

1. entity

GEILKELPEG FDKETVRKQA MEDIEIAQSK DYESWKSRFT KDLQSSLTEE SYDSYLKILE KQGEFKEFGK CTYLGQIKDN KKYGGVIIVV KYEEGNVNYS LAYDEDMNLV SFTM

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-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	D2O	[U-99% 2H]		95 %
6	H2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: 2.59 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 2.59 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.05 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MC8, Strand ID: A Detail

Release date

2013-10-20

Citation

NMR structure of a hypothetical protein RUMGNA_01855 from Ruminococcus gnavus ATCC 29149
Dutta, S.K., Serrano, P., Geralt, M., Wuthrich, K.
Not known

Related entities 1. hypothetical protein, : 1 : 1 entities Detail

Experiments performed 7 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 6.0

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

2 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	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	D2O	[U-99% 2H]		95 %
6	H2O	natural abundance		5 %

3 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	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	D2O	[U-99% 2H]		95 %
6	H2O	natural abundance		5 %

4 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	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	D2O	[U-99% 2H]		95 %
6	H2O	natural abundance		5 %

5 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	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	D2O	[U-99% 2H]		95 %
6	H2O	natural abundance		5 %

6 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	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	D2O	[U-99% 2H]		95 %
6	H2O	natural abundance		5 %

7 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	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	D2O	[U-99% 2H]		95 %
6	H2O	natural abundance		5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19431_2mc8.nef
Input source #2: Coordindates	2mc8.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
GEILKELPEGFDKETVRKQAMEDIEIAQSKDYESWKSRFTKDLQSSLTEESYDSYLKILEKQGEFKEFGKCTYLGQIKDNKKYGGVIIVVKYEEGNVNYS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GEILKELPEGFDKETVRKQAMEDIEIAQSKDYESWKSRFTKDLQSSLTEESYDSYLKILEKQGEFKEFGKCTYLGQIKDNKKYGGVIIVVKYEEGNVNYS

-------110----
LAYDEDMNLVSFTM
||||||||||||||
LAYDEDMNLVSFTM

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	114	0	0	100.0

Content subtype: combined_19431_2mc8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1217		99.1 (chain: A, length: 114)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2290 (1)	noe	99.1 (chain: A, length: 114)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 99.1%
- Total number of assignments
  - ¹H chemical shifts: 693
  - ¹³C chemical shifts: 403
  - ¹⁵N chemical shifts: 121
- 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: 114, Sequence coverage: 99.1%
- Total number of restraints: 2286
- Weight of restraints: 1.0 (2286)
- Potential type of restraints: upper-bound-parabolic (2286)
- 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 human gut microbiome secreted protein, hypothetical protein