BMRB Entry 15816

Name: Solution NMR Structure of Allochromatium vinosum DsrR: Northeast Structural Genomics Consortium Target OP5
Published: 2008-07-03

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PDB ID: 2k4z
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15816
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

2008-06-22

Original release date:

2008-07-03

Authors:

Cort, John; Dahl, Christiane; Grimm, Frauke; Kennedy, Michael

Citation:

Citation: Dahl, Christiane; Cort, John; Grimm, Frauke. "Solution NMR Structure of the IscA-like Protein DsrR Involved in Sulfur Oxidation in Allochromatium vinosum" .

Assembly members:

Assembly members:
DsrR, polymer, 125 residues, 13748.496 Da.

Natural source:

Natural source: Common Name: Allochromatium vinosum Taxonomy ID: 1049 Superkingdom: Bacteria Kingdom: not available Genus/species: Allochromatium vinosum

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET15

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DsrR: MGSSHHHHHHSSGLVPRGSH MMFKLTPAAAEQVLKAAKQG GTEGMCLRLAAGRNPDGSID YRMGFDDLTEDDIRLTSEGV EIVIAPDYVSLLDQTTLDYV ELEPGQFHFIFLNPRDPTYR PPSGG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	431
15N chemical shifts	101
1H chemical shifts	686

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DsrR	1

Entities:

Entity 1, DsrR 125 residues - 13748.496 Da.

sequence begins with residue -20. The first residue of the native DsrR sequence is Met 1

1

MET

GLY

SER

HIS

2

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

3

MET

PHE

LYS

LEU

THR

PRO

ALA

4

GLU

GLN

VAL

LEU

LYS

ALA

LYS

GLN

GLY

5

GLY

THR

GLU

GLY

MET

CYS

LEU

ARG

LEU

ALA

6

ALA

GLY

ARG

ASN

PRO

ASP

GLY

SER

ILE

ASP

7

TYR

ARG

MET

GLY

PHE

ASP

LEU

THR

GLU

8

ASP

ILE

ARG

LEU

THR

SER

GLU

GLY

VAL

9

GLU

ILE

VAL

ILE

ALA

PRO

ASP

TYR

VAL

SER

10

LEU

ASP

GLN

THR

LEU

ASP

TYR

VAL

11

GLU

LEU

GLU

PRO

GLY

GLN

PHE

HIS

PHE

ILE

12

PHE

LEU

ASN

PRO

ARG

ASP

PRO

THR

TYR

ARG

13

PRO

SER

GLY

Samples:

sample_1: DsrR, [U-10% 13C; U-100% 15N], 1 ± 0.1 mM; H2O 93%; D2O 7%; Tris HCl 50 mM; sodium chloride 500 mM; DTT 5 mM; sodium azide 0.02%

sample_2: DsrR, [U-100% 13C; U-100% 15N], 1 ± 0.1 mM; D2O 100%; Tris HCl 50 mM; sodium chloride 500 mM; DTT 5 mM; sodium azide 0.02%

sample_3: DsrR, [U-100% 13C; U-100% 15N], 1 ± 0.1 mM; H2O 93%; D2O 7%; Tris HCl 50 mM; sodium chloride 500 mM; DTT 5 mM; sodium azide 0.02%

sample_conditions_1: ionic strength: 625 mM; pH: 7.4; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
4D 1H-13C-13C-1H HMQC NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1

Software:

FELIX, Accelrys Software Inc. - data analysis, processing

AutoStruct, Huang, Tejero, Powers and Montelione - structure solution

SPARKY, Goddard - chemical shift assignment

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 750 MHz

PDB	2K4Z
GB	AAG13087 ADC62203
REF	WP_043796041