BMRB Entry 15902

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PDB ID: 2k75
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/BMR15902
MolProbity Validation Chart

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Nicholas Rego and David Koes
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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 domain of Ta0387 from Thermoplasma acidophilum. Northeast Structural Genomics Consortium target TaR80b.

Deposition date:

2008-08-01

Original release date:

2008-08-13

Authors:

Ramelot, Theresa; Ding, Keyang; Lee, Dan; Jiang, Mei; Ciccosanti, Colleen; Xiao, Rong; Nair, Rajesh; Everett, John; Swapna, G.V.T; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano; Kennedy, Michael

Citation:

Citation: Ramelot, Theresa; Ding, Keyang; Lee, Dan; Jiang, Mei; Ciccosanti, Colleen; Xiao, Rong; Nair, Rajesh; Everett, John; Swapna, G.V.T; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano; Kennedy, Michael. "Solution NMR structure of the OB domain of Ta0387 from Thermoplasma acidophilum." .

Assembly members:

Assembly members:
Ta0387, polymer, 106 residues, 11896.298 Da.

Natural source:

Natural source: Common Name: Thermoplasma acidophilum Taxonomy ID: 2303 Superkingdom: Archaea Kingdom: not available Genus/species: Thermoplasma acidophilum

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET21-23C

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Ta0387: SDLVKIRDVSLSTPYVSVIG KITGIHKKEYESDGTTKSVY QGYIEDDTARIRISSFGKQL QDSDVVRIDNARVAQFNGYL SLSVGDSSRIESVNVNIPLE HHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
spectral_peak_list

Data type	Count
13C chemical shifts	467
15N chemical shifts	117
1H chemical shifts	733

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Ta0387	1

Entities:

Entity 1, Ta0387 106 residues - 11896.298 Da.

residues 105-202 of Ta0387

1

SER

ASP

LEU

VAL

LYS

ILE

ARG

ASP

VAL

SER

2

LEU

SER

THR

PRO

TYR

VAL

SER

VAL

ILE

GLY

3

LYS

ILE

THR

GLY

ILE

HIS

LYS

GLU

TYR

4

GLU

SER

ASP

GLY

THR

LYS

SER

VAL

TYR

5

GLN

GLY

TYR

ILE

GLU

ASP

THR

ALA

ARG

6

ILE

ARG

ILE

SER

PHE

GLY

LYS

GLN

LEU

7

GLN

ASP

SER

ASP

VAL

ARG

ILE

ASP

ASN

8

ALA

ARG

VAL

ALA

GLN

PHE

ASN

GLY

TYR

LEU

9

SER

LEU

SER

VAL

GLY

ASP

SER

ARG

ILE

10

GLU

SER

VAL

ASN

VAL

ASN

ILE

PRO

LEU

GLU

11

HIS

Samples:

NC_sample: ammonium acetate 20 ± 1 mM; sodium chloride 100 ± 5 mM; DTT 10 ± 0.5 mM; calcium chloride 5 ± 0.05 mM; sodium azide 0.02 ± 0.001 %; protein, [U-100% 13C; U-100% 15N], 1.0 ± 0.1 mM; D2O 5%; H2O 95%

NC5_sample: ammonium acetate 20 ± 1 mM; sodium chloride 100 ± 5 mM; DTT 10 ± 0.5 mM; calcium chloride 5 ± 0.05 mM; sodium azide 0.02 ± 0.001 %; protein, [U-5% 13C; U-100% 15N], 1.3 ± .1 mM; D2O 5%; H2O 95%

NC_sample_in_D2O: ammonium acetate 20 ± 1 mM; sodium chloride 100 ± 5 mM; DTT 10 ± 0.5 mM; calcium chloride 5 ± 0.05 mM; sodium azide 0.02 ± 0.001 %; protein, [U-100% 13C; U-100% 15N], 1.0 ± 0.1 mM; D2O 100%

sample_conditions_1: ionic strength: 100 mM; pH: 4.5; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	NC_sample	isotropic	sample_conditions_1
2D 1H-13C HSQC	NC_sample	isotropic	sample_conditions_1
2D 1H-13C HSQC	NC5_sample	isotropic	sample_conditions_1
3D 1H-15N NOESY	NC_sample	isotropic	sample_conditions_1
3D 1H-13C NOESY	NC_sample	isotropic	sample_conditions_1
3D HNCO	NC_sample	isotropic	sample_conditions_1
3D HNCA	NC_sample	isotropic	sample_conditions_1
3D HNCACB	NC_sample	isotropic	sample_conditions_1
3D CBCA(CO)NH	NC_sample	isotropic	sample_conditions_1
3D HBHA(CO)NH	NC_sample	isotropic	sample_conditions_1
3D HCCH-TOCSY	NC_sample	isotropic	sample_conditions_1
3D HCCH-COSY	NC_sample	isotropic	sample_conditions_1
3D H(CCO)NH	NC_sample	isotropic	sample_conditions_1
3D C(CO)NH	NC_sample	isotropic	sample_conditions_1
2D 1H-15N HSQC (1 hr)	NC_sample_in_D2O	isotropic	sample_conditions_1
2D 1H-13C HSQC	NC_sample_in_D2O	isotropic	sample_conditions_1
3D 1H-13C NOESY	NC_sample_in_D2O	isotropic	sample_conditions_1
4D CC NOESY	NC_sample_in_D2O	isotropic	sample_conditions_1
3D 1H-13C NOESY	NC_sample	isotropic	sample_conditions_1
2D 1H-15N HSQC (1 day)	NC_sample_in_D2O	isotropic	sample_conditions_1

Software:

AutoAssign v2.3.0, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment

NMRPipe vlinux9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

VNMR v6.1C, Varian - collection

TOPSPIN v2.1, Bruker Biospin - collection

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

X-PLOR NIH v2.20.0, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

SPARKY v3.113, Goddard - data analysis

PSVS v1.3, Bhattacharya and Montelione - structure solution

NMR spectrometers:

Varian INOVA 600 MHz
Bruker AvanceIII 850 MHz

SWS	Q9HL44
UNP	Q9HL44
PDB	2K75
AlphaFold	Q9HL44