BMRB Entry 16283

Name: 1.7-mm microcryoprobe solution NMR structure of an O6-methylguanine DNA methyltransferase family protein from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium target VpR247.
Published: 2010-09-17

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PDB ID: 2kim
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16283
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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:

1.7-mm microcryoprobe solution NMR structure of an O6-methylguanine DNA methyltransferase family protein from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium target VpR247.

Deposition date:

2009-05-07

Original release date:

2010-09-17

Authors:

Aramini, James; Belote, Rachel; Ciccosanti, Colleen; Jiang, Mei; Rost, Burkhard; Nair, Rajesh; Swapna, G.; Acton, Thomas; Xiao, Rong; Everett, John; Montelione, Gaetano

Citation:

Citation: Aramini, James; Belote, Rachel; Ciccosanti, Colleen; Jiang, Mei; Rost, Burkhard; Nair, Rajesh; Swapna, G.; Acton, Thomas; Xiao, Rong; Everett, John; Montelione, Gaetano. "Solution NMR structure of an O6-methylguanine DNA methyltransferase family protein from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium target VpR247." .

Assembly members:

Assembly members:
VpR247, polymer, 108 residues, 12341.439 Da.

Natural source:

Natural source: Common Name: Vibrio parahaemolyticus Taxonomy ID: 670 Superkingdom: Bacteria Kingdom: not available Genus/species: Vibrio parahaemolyticus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: VpR247-21.9

Entity Sequences (FASTA):

Entity Sequences (FASTA):
VpR247: MDQFLVQIFAVIHQIPKGKV STYGEIAKMAGYPGYARHVG KALGNLPEGSKLPWFRVINS QGKISLKGRDLDRQKQKLEA EGIEVSEIGKIALRKYKWQP LEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	485
15N chemical shifts	104
1H chemical shifts	768

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	VpR247	1

Entities:

Entity 1, VpR247 108 residues - 12341.439 Da.

1

MET

ASP

GLN

PHE

LEU

VAL

GLN

ILE

PHE

ALA

2

VAL

ILE

HIS

GLN

ILE

PRO

LYS

GLY

LYS

VAL

3

SER

THR

TYR

GLY

GLU

ILE

ALA

LYS

MET

ALA

4

GLY

TYR

PRO

GLY

TYR

ALA

ARG

HIS

VAL

GLY

5

LYS

ALA

LEU

GLY

ASN

LEU

PRO

GLU

GLY

SER

6

LYS

LEU

PRO

TRP

PHE

ARG

VAL

ILE

ASN

SER

7

GLN

GLY

LYS

ILE

SER

LEU

LYS

GLY

ARG

ASP

8

LEU

ASP

ARG

GLN

LYS

GLN

LYS

LEU

GLU

ALA

9

GLU

GLY

ILE

GLU

VAL

SER

GLU

ILE

GLY

LYS

10

ILE

ALA

LEU

ARG

LYS

TYR

LYS

TRP

GLN

PRO

11

LEU

GLU

HIS

Samples:

sample_1: VpR247, [U-100% 13C; U-100% 15N], 0.94 mM; MES 20 mM; sodium chloride 200 mM; calcium chloride 5 mM; DTT 10 mM; sodium azide 0.02%; DSS 50 uM; H2O 90%; D2O 10%

sample_2: VpR247, [U-5% 13C; U-100% 15N], 0.92 mM; MES 20 mM; sodium chloride 200 mM; calcium chloride 5 mM; DTT 10 mM; sodium azide 0.02%; DSS 50 uM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.2 M; pH: 6.5; pressure: 1 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 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HNCA	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 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
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
2D 1H-15N hetNOE	sample_1	isotropic	sample_conditions_1
1D 1H-15N T1 and T2	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC high res. (L/V methyl stereoassignment)	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - collection, data analysis

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

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

PINE v1.0, 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 v1.2, 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

MolProbity v3.15, Richardson - structure quality analysis

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

NMR spectrometers:

Bruker Avance 600 MHz

BMRB	16272
PDB	2KIF 2KIM
DBJ	BAC59214
GB	AGB09412 AGQ90485 AGQ98830 AHI99009 AKU55569
REF	NP_797330 WP_005461131 WP_005481834 WP_021449579 WP_025501692
SP	A6B4U8
AlphaFold	A6B4U8