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Found 1 Document (0.695 seconds)

BMRB: 15816

2K4Z

Solution NMR Structure of Allochromatium vinosum DsrR: Northeast Structural Genomics Consortium Target OP5

Authors

Cort, J.R., Dahl, C., Grimm, F., Kennedy, M.A.

Assembly

DsrR

Entity

1. DsrR (polymer, Thiol state: all free), 125 monomers, 13730.24 Da Detail

MGSSHHHHHH SSGLVPRGSH MMFKLTPAAA EQVLKAAKQG GTEGMCLRLA AGRNPDGSID YRMGFDDLTE DDIRLTSEGV EIVIAPDYVS LLDQTTLDYV ELEPGQFHFI FLNPRDPTYR PPSGG

Formula weight

13730.24 Da

Source organism

Allochromatium vinosum

Exptl. method

solution NMR

Refine. method

molecular dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 84.0 %, Completeness: 79.9 %, Completeness (bb): 81.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	79.9 % (1114 of 1395)	80.1 % (578 of 722)	78.8 % (434 of 551)	83.6 % (102 of 122)
Backbone	81.7 % (598 of 732)	81.9 % (208 of 254)	81.2 % (294 of 362)	82.8 % (96 of 116)
Sidechain	78.7 % (610 of 775)	79.1 % (370 of 468)	77.7 % (234 of 301)	100.0 % (6 of 6)
Aromatic	41.2 % (47 of 114)	43.9 % (25 of 57)	38.6 % (22 of 57)
Methyl	93.4 % (114 of 122)	93.4 % (57 of 61)	93.4 % (57 of 61)

1. DsrR

MGSSHHHHHH SSGLVPRGSH MMFKLTPAAA EQVLKAAKQG GTEGMCLRLA AGRNPDGSID YRMGFDDLTE DDIRLTSEGV EIVIAPDYVS LLDQTTLDYV ELEPGQFHFI FLNPRDPTYR PPSGG

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	DsrR	[U-10% 13C; U-100% 15N]	1 (±0.1) mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %
4	Tris HCl	natural abundance	50 mM
5	sodium chloride	natural abundance	500 mM
6	DTT	natural abundance	5 mM
7	sodium azide	natural abundance	0.02 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
8	DsrR	[U-100% 13C; U-100% 15N]	1 (±0.1) mM
9	D2O	natural abundance	100 %
10	Tris HCl	natural abundance	50 mM
11	sodium chloride	natural abundance	500 mM
12	DTT	natural abundance	5 mM
13	sodium azide	natural abundance	0.02 %

Sample #3

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
14	DsrR	[U-100% 13C; U-100% 15N]	1 (±0.1) mM
15	H2O	natural abundance	93 %
16	D2O	natural abundance	7 %
17	Tris HCl	natural abundance	50 mM
18	sodium chloride	natural abundance	500 mM
19	DTT	natural abundance	5 mM
20	sodium azide	natural abundance	0.02 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.1 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.1 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: 0.42 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K4Z, Strand ID: A Detail

Release date

2008-07-02

Citation

DsrR, a novel IscA-like protein lacking iron- and Fe-S-binding functions, involved in the regulation of sulfur oxidation in Allochromatium vinosum
Dahl, C., Cort, J.R., Grimm, F.
J. Bacteriol. (2010), 192, 1652-1661, PubMed 20061482 , DOI 10.1128/JB.01269-09 , Abstract

Related entities 1. DsrR, : 1 : 8 entities Detail

Experiments performed 14 experiments Detail

1 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	DsrR	[U-10% 13C; U-100% 15N]	1 (±0.1) mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %
4	Tris HCl	natural abundance	50 mM
5	sodium chloride	natural abundance	500 mM
6	DTT	natural abundance	5 mM
7	sodium azide	natural abundance	0.02 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	DsrR	[U-10% 13C; U-100% 15N]	1 (±0.1) mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %
4	Tris HCl	natural abundance	50 mM
5	sodium chloride	natural abundance	500 mM
6	DTT	natural abundance	5 mM
7	sodium azide	natural abundance	0.02 %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	DsrR	[U-10% 13C; U-100% 15N]	1 (±0.1) mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %
4	Tris HCl	natural abundance	50 mM
5	sodium chloride	natural abundance	500 mM
6	DTT	natural abundance	5 mM
7	sodium azide	natural abundance	0.02 %

4 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	DsrR	[U-10% 13C; U-100% 15N]	1 (±0.1) mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %
4	Tris HCl	natural abundance	50 mM
5	sodium chloride	natural abundance	500 mM
6	DTT	natural abundance	5 mM
7	sodium azide	natural abundance	0.02 %

5 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	DsrR	[U-10% 13C; U-100% 15N]	1 (±0.1) mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %
4	Tris HCl	natural abundance	50 mM
5	sodium chloride	natural abundance	500 mM
6	DTT	natural abundance	5 mM
7	sodium azide	natural abundance	0.02 %

6 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	DsrR	[U-10% 13C; U-100% 15N]	1 (±0.1) mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %
4	Tris HCl	natural abundance	50 mM
5	sodium chloride	natural abundance	500 mM
6	DTT	natural abundance	5 mM
7	sodium azide	natural abundance	0.02 %

7 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	DsrR	[U-10% 13C; U-100% 15N]	1 (±0.1) mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %
4	Tris HCl	natural abundance	50 mM
5	sodium chloride	natural abundance	500 mM
6	DTT	natural abundance	5 mM
7	sodium azide	natural abundance	0.02 %

8 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	DsrR	[U-10% 13C; U-100% 15N]	1 (±0.1) mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %
4	Tris HCl	natural abundance	50 mM
5	sodium chloride	natural abundance	500 mM
6	DTT	natural abundance	5 mM
7	sodium azide	natural abundance	0.02 %

9 3D HCCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	DsrR	[U-10% 13C; U-100% 15N]	1 (±0.1) mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %
4	Tris HCl	natural abundance	50 mM
5	sodium chloride	natural abundance	500 mM
6	DTT	natural abundance	5 mM
7	sodium azide	natural abundance	0.02 %

10 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	DsrR	[U-10% 13C; U-100% 15N]	1 (±0.1) mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %
4	Tris HCl	natural abundance	50 mM
5	sodium chloride	natural abundance	500 mM
6	DTT	natural abundance	5 mM
7	sodium azide	natural abundance	0.02 %

11 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	DsrR	[U-10% 13C; U-100% 15N]	1 (±0.1) mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %
4	Tris HCl	natural abundance	50 mM
5	sodium chloride	natural abundance	500 mM
6	DTT	natural abundance	5 mM
7	sodium azide	natural abundance	0.02 %

12 4D 1H-13C-13C-1H HMQC NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
8	DsrR	[U-100% 13C; U-100% 15N]	1 (±0.1) mM
9	D2O	natural abundance	100 %
10	Tris HCl	natural abundance	50 mM
11	sodium chloride	natural abundance	500 mM
12	DTT	natural abundance	5 mM
13	sodium azide	natural abundance	0.02 %

13 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
14	DsrR	[U-100% 13C; U-100% 15N]	1 (±0.1) mM
15	H2O	natural abundance	93 %
16	D2O	natural abundance	7 %
17	Tris HCl	natural abundance	50 mM
18	sodium chloride	natural abundance	500 mM
19	DTT	natural abundance	5 mM
20	sodium azide	natural abundance	0.02 %

14 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Concentration
8	DsrR	[U-100% 13C; U-100% 15N]	1 (±0.1) mM
9	D2O	natural abundance	100 %
10	Tris HCl	natural abundance	50 mM
11	sodium chloride	natural abundance	500 mM
12	DTT	natural abundance	5 mM
13	sodium azide	natural abundance	0.02 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15816_2k4z.nef
Input source #2: Coordindates	2k4z.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--------8
MGSSHHHHHHSSGLVPRGSHMMFKLTPAAAEQVLKAAKQGGTEGMCLRLAAGRNPDGSIDYRMGFDDLTEDDIRLTSEGVEIVIAPDYVSLLDQTTLDYV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGLVPRGSHMMFKLTPAAAEQVLKAAKQGGTEGMCLRLAAGRNPDGSIDYRMGFDDLTEDDIRLTSEGVEIVIAPDYVSLLDQTTLDYV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0--------90-------100----
ELEPGQFHFIFLNPRDPTYRPPSGG
|||||||||||||||||||||||||
ELEPGQFHFIFLNPRDPTYRPPSGG
-------110-------120-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	125	0	0	100.0

Content subtype: combined_15816_2k4z.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1096		81.6 (chain: A, length: 125)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1316 (1)	noe	79.2 (chain: A, length: 125)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	41 (1)	hbond	22.4 (chain: A, length: 125)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	74 (74)	.	49.6 (chain: A, length: 125)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 81.6%
- Total number of assignments
  - ¹H chemical shifts: 564
  - ¹³C chemical shifts: 431
  - ¹⁵N chemical shifts: 101
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
5	THR	HG1	5.75
11	GLN	CD	178.4
18	GLN	CD	180.1
33	ASN	CG	176.6
73	GLN	CD	180.7
85	GLN	CD	180.3
92	ASN	CG	175.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	722	563	78.0
¹³C chemical shifts	551	425	77.1
¹⁵N chemical shifts	129	101	78.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	254	203	79.9
¹³C chemical shifts	250	195	78.0
¹⁵N chemical shifts	116	94	81.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	468	360	76.9
¹³C chemical shifts	301	230	76.4
¹⁵N chemical shifts	13	7	53.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	66	61	92.4
¹³C chemical shifts	66	61	92.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	57	22	38.6
¹³C chemical shifts	57	22	38.6

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 79.2%
- Total number of restraints: 1316
- Weight of restraints: 1.0 (1316)
- Potential type of restraints: square-well-parabolic (1316)
- Range of distance target values: 2.3, 3.65 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 22.4%
  - Total number of restraints: 41
  - Weight of restraints: 1.0 (41)
  - Potential type of restraints: square-well-parabolic (41)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 49.6%
- Total number of restraints: 74
- Total number of restraints per polymer type: 74
- Weight of restraints: 1.0 (74)
- Potential type of restraints: square-well-parabolic (74)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords Allochromatium vinosum, dsr gene cluster, DsrR, IscA, sulfur oxidation, IscA/SufA/HesB like fold

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Found 1 Document (0.695 seconds)

BMRB: 15816

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. DsrR, : 1 : 8 entities Detail

Experiments performed 14 experiments Detail

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NMR combined restraints 5 contents Detail