BMRB Entry 16096

Name: SOLUTION NMR STRUCTURE OF THE OB-FOLD DOMAIN OF HEME CHAPERONE CCME FROM DESULFOVIBRIO VULGARIS. NORTHEAST STRUCTURAL GENOMICS TARGET DVR115G.
Published: 2009-05-07

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PDB ID: 2kct
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16096
MolProbity Validation Chart

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

SOLUTION NMR STRUCTURE OF THE OB-FOLD DOMAIN OF HEME CHAPERONE CCME FROM DESULFOVIBRIO VULGARIS. NORTHEAST STRUCTURAL GENOMICS TARGET DVR115G.

Deposition date:

2008-12-29

Original release date:

2009-05-07

Authors:

Aramini, James; Rossi, Paolo; Lee, Hsiau-Wei; Alexander, Lemak; Wang, Huang; Foote, Erica; Jiang, Mei; Xiao, Rong; Nair, Rajesh; Swapna, G.; Acton, Thomas; Rost, Burkhard; Everett, John; Montelione, Gaetano

Citation:

Citation: Aramini, James; Rossi, Paolo; Lee, Hsiau-Wei; Alexander, Lemak; Wang, Huang; Foote, Erica; Jiang, Mei; Xiao, Rong; Nair, Rajesh; Swapna, G.; Acton, Thomas; Rost, Burkhard; Everett, John; Montelione, Gaetano. "SOLUTION NMR STRUCTURE OF THE OB-FOLD DOMAIN OF HEME CHAPERONE CCME FROM DESULFOVIBRIO VULGARIS. NORTHEAST STRUCTURAL GENOMICS TARGET DVR115G." .

Assembly members:

Assembly members:
DvR115G, polymer, 94 residues, 10375.994 Da.

Natural source:

Natural source: Common Name: Desulfovibrio vulgaris Taxonomy ID: 881 Superkingdom: Bacteria Kingdom: not available Genus/species: Desulfovibrio vulgaris

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: DvR115G-21.2

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DvR115G: MATPQDKLHTVRLFGTVAAD GLTMLDGAPGVRFRLEDKDN TSKTVWVLYKGAVPDTFKPG VEVIIEGGLAPGEDTFKART LMTKCPLEHHHHHH

Data sets:

RDCs
- RDC_list_1
assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	392
15N chemical shifts	87
1H chemical shifts	618
residual dipolar couplings	49

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DvR115G	1

Entities:

Entity 1, DvR115G 94 residues - 10375.994 Da.

The N-terminal Met and C-terminal affinity tag (LEHHHHHH) are cloning artefacts.

1

MET

ALA

THR

PRO

GLN

ASP

LYS

LEU

HIS

THR

2

VAL

ARG

LEU

PHE

GLY

THR

VAL

ALA

ASP

3

GLY

LEU

THR

MET

LEU

ASP

GLY

ALA

PRO

GLY

4

VAL

ARG

PHE

ARG

LEU

GLU

ASP

LYS

ASP

ASN

5

THR

SER

LYS

THR

VAL

TRP

VAL

LEU

TYR

LYS

6

GLY

ALA

VAL

PRO

ASP

THR

PHE

LYS

PRO

GLY

7

VAL

GLU

VAL

ILE

GLU

GLY

LEU

ALA

8

PRO

GLY

GLU

ASP

THR

PHE

LYS

ALA

ARG

THR

9

LEU

MET

THR

LYS

CYS

PRO

LEU

GLU

HIS

10

HIS

Samples:

sample_1: DvR115G, [U-100% 13C; U-100% 15N], 1.3 mM; ammonium acetate 20 mM; sodium chloride 200 mM; calcium chloride 5 mM; DTT 10 mM; sodium azide 0.02%; DSS 50 uM

sample_2: DvR115G, [U-5% 13C; U-100% 15N], 0.56 mM; ammonium acetate 20 mM; sodium chloride 200 mM; calcium chloride 5 mM; DTT 10 mM; sodium azide 0.02%; DSS 50 uM

sample_3: DvR115G, [U-5% 13C; U-100% 15N], 70 %v/v; PEG/hexanol 4.2%

sample_conditions_1: ionic strength: 0.2 M; pH: 4.5; pressure: 1.0 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D simultaneous CN NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC high res. (L/V methyl stereoassignment)	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	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 HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D C(CO)NH TOCSY	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY aliphatic	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY aliphatic	sample_1	isotropic	sample_conditions_1
3D (H)CCH-TOCSY aliphatic	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
2D 1H-15N hetNOE	sample_1	isotropic	sample_conditions_1
1D 1H-15N T1 and T2	sample_1	isotropic	sample_conditions_1
2D 1H-15N TROSY (for N-H RDCs)	sample_3	anisotropic	sample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - N15 T1/T2 data analysis, collection

VNMRJ v2.1B, Varian - collection

NMRPipe v2.3, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.112, Goddard - data analysis, peak picking

PINE, Bahrami, Markley, Assadi, and Eghbalnia - chemical shift assignment

AutoAssign v2.4.0, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment, validation

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

AutoStruct v2.2.1, Huang, Tejero, Powers and Montelione - RPF analysis

PSVS v1.3, Bhattacharya and Montelione - structure quality analysis

PDBStat v5.1, Tejero and Montelione - PDB coordinate analysis

PALES, Zweckstetter and Bax - Prediction of molecular alignment

NMR spectrometers:

Bruker Avance 800 MHz
Varian INOVA 600 MHz
Bruker Avance 600 MHz