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BMRB: 25085

2MRM

Solution structure of the rhodanese domain of YgaP from E. coli

Authors

Wang, W., Zhou, P., Tian, C., Wu, F.

Assembly

rhodanese domain of YgaP

Entity

1. rhodanese domain of YgaP (polymer, Thiol state: all free), 114 monomers, 12598.21 Da Detail

MHHHHHHMAL TTISPHDAQE LIARGAKLID IRDADEYLRE HIPEADLAPL SVLEQSGLPA KLRHEQIIFH CQAGKRTSNN ADKLAAIAAP AEIFLLEDGI DGWKRAGLPV AVNK

Formula weight

12598.21 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.9 %, Completeness: 84.4 %, Completeness (bb): 91.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.4 % (1097 of 1300)	85.9 % (578 of 673)	81.4 % (416 of 511)	88.8 % (103 of 116)
Backbone	91.4 % (614 of 672)	92.1 % (210 of 228)	90.5 % (304 of 336)	92.6 % (100 of 108)
Sidechain	78.1 % (575 of 736)	82.0 % (365 of 445)	73.5 % (208 of 283)	25.0 % (2 of 8)
Aromatic	5.0 % (4 of 80)	7.5 % (3 of 40)	0.0 % (0 of 39)	100.0 % (1 of 1)
Methyl	89.6 % (129 of 144)	97.2 % (70 of 72)	81.9 % (59 of 72)

1. YgaP

MHHHHHHMAL TTISPHDAQE LIARGAKLID IRDADEYLRE HIPEADLAPL SVLEQSGLPA KLRHEQIIFH CQAGKRTSNN ADKLAAIAAP AEIFLLEDGI DGWKRAGLPV AVNK

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	YgaP	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium chloride	natural abundance		50 mM
3	TRIS	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
6	YgaP	[U-100% 13C; U-100% 15N]		0.5 mM
7	sodium chloride	natural abundance		50 mM
8	TRIS	natural abundance		20 mM
9	D2O	natural abundance		100 %

LACS Plot; CA

Referencing offset: -0.22 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.22 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.0 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.19 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2MRM, Strand ID: A Detail

Release date

2014-09-18

Citation

Fast conformational exchange between the sulfur-free and persulfide-bound rhodanese domain of E. coli YgaP
Wang, W., Zhou, P., He, Y., Yu, L., Xiong, Y., Tian, C., Wu, F.
Biochem. Biophys. Res. Commun. (2014), 452, 817-821, PubMed 25204500 , DOI 10.1016/j.bbrc.2014.09.002 , Abstract

Related entities 1. rhodanese domain of YgaP, : 1 : 63 entities Detail

Interaction partners 1. rhodanese domain of YgaP, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	YgaP	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium chloride	natural abundance		50 mM
3	TRIS	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

2 3D CBCA(CO)NH

Instrument

Varian INOVA - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	YgaP	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium chloride	natural abundance		50 mM
3	TRIS	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

3 3D HNCACB

Instrument

Varian INOVA - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	YgaP	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium chloride	natural abundance		50 mM
3	TRIS	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

4 3D HNCO

Instrument

Varian INOVA - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	YgaP	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium chloride	natural abundance		50 mM
3	TRIS	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

5 3D HBHA(CO)NH

Instrument

Varian INOVA - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	YgaP	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium chloride	natural abundance		50 mM
3	TRIS	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

6 3D H(CCO)NH

Instrument

Varian INOVA - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	YgaP	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium chloride	natural abundance		50 mM
3	TRIS	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

7 3D C(CO)NH

Instrument

Varian INOVA - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	YgaP	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium chloride	natural abundance		50 mM
3	TRIS	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

8 3D 1H-15N NOESY

Instrument

Varian INOVA - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	YgaP	[U-100% 13C; U-100% 15N]		0.5 mM
2	sodium chloride	natural abundance		50 mM
3	TRIS	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

9 3D HCCH-TOCSY

Instrument

Varian INOVA - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
6	YgaP	[U-100% 13C; U-100% 15N]		0.5 mM
7	sodium chloride	natural abundance		50 mM
8	TRIS	natural abundance		20 mM
9	D2O	natural abundance		100 %

10 3D HCCH-COSY

Instrument

Varian INOVA - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
6	YgaP	[U-100% 13C; U-100% 15N]		0.5 mM
7	sodium chloride	natural abundance		50 mM
8	TRIS	natural abundance		20 mM
9	D2O	natural abundance		100 %

11 3D 1H-13C NOESY

Instrument

Varian INOVA - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
6	YgaP	[U-100% 13C; U-100% 15N]		0.5 mM
7	sodium chloride	natural abundance		50 mM
8	TRIS	natural abundance		20 mM
9	D2O	natural abundance		100 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25085_2mrm.nef
Input source #2: Coordindates	2mrm.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---
MHHHHHHMALTTISPHDAQELIARGAKLIDIRDADEYLREHIPEADLAPLSVLEQSGLPAKLRHEQIIFHCQAGKRTSNNADKLAAIAAPAEIFLLEDGI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MHHHHHHMALTTISPHDAQELIARGAKLIDIRDADEYLREHIPEADLAPLSVLEQSGLPAKLRHEQIIFHCQAGKRTSNNADKLAAIAAPAEIFLLEDGI
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

----100-------
DGWKRAGLPVAVNK
||||||||||||||
DGWKRAGLPVAVNK
-------110----

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_25085_2mrm.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1097		93.9 (chain: A, length: 114)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	2157 (1)	noe	93.9 (chain: A, length: 114)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	126 (126)	.	75.4 (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: 93.9%
- Total number of assignments
  - ¹H chemical shifts: 580
  - ¹³C chemical shifts: 415
  - ¹⁵N chemical shifts: 102
- 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: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 93.9%
- Total number of restraints: 2146
- Weight of restraints: 1.0 (2146)
- Potential type of restraints: square-well-parabolic (2146)
- Range of distance target values: 2.4, 3.9 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 75.4%
- Total number of restraints: 126
- Total number of restraints per polymer type: 126
- Weight of restraints: 1.0 (126)
- Potential type of restraints: square-well-parabolic (126)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords rhodanese domain, YgaP, E. coli, Integral Membrane Protein