BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 16272

Title: Solution NMR structure of an O6-methylguanine DNA methyltransferase family protein from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium target VpR247.

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

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."  Not known ., .-..

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

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

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

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

Data sets:
Data typeCount
13C chemical shifts486
15N chemical shifts104
1H chemical shifts768

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1VpR2471

Entities:

Entity 1, VpR247 108 residues - 12341.439 Da.

1   METASPGLNPHELEUVALGLNILEPHEALA
2   VALILEHISGLNILEPROLYSGLYLYSVAL
3   SERTHRTYRGLYGLUILEALALYSMETALA
4   GLYTYRPROGLYTYRALAARGHISVALGLY
5   LYSALALEUGLYASNLEUPROGLUGLYSER
6   LYSLEUPROTRPPHEARGVALILEASNSER
7   GLNGLYLYSILESERLEULYSGLYARGASP
8   LEUASPARGGLNLYSGLNLYSLEUGLUALA
9   GLUGLYILEGLUVALSERGLUILEGLYLYS
10   ILEALALEUARGLYSTYRLYSTRPGLNPRO
11   LEUGLUHISHISHISHISHISHIS

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; H20 90%; D20 10%

sample_2: 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; H20 90%; D20 10%

sample_3: 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; H20 90%; D20 10%

sample_conditions_1: ionic strength: 0.2 M; pH: 6.5; pressure: 1.0 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D simultaneous CN NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HN(CA)COsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D HBHA(CO)NHsample_2isotropicsample_conditions_1
3D HCCH-COSY aliphaticsample_2isotropicsample_conditions_1
3D HCCH-TOCSY aliphaticsample_2isotropicsample_conditions_1
3D (H)CCH-TOCSY aliphaticsample_2isotropicsample_conditions_1
3D HNHAsample_2isotropicsample_conditions_1
3D HN(CO)CAsample_2isotropicsample_conditions_1
2D 1H-15N hetNOEsample_2isotropicsample_conditions_1
1D 1H-15N T1 and T2sample_3isotropicsample_conditions_1
2D 1H-13C HSQC high res. (L/V methyl stereoassignment)sample_3isotropicsample_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 800 MHz
  • Bruker Avance 600 MHz

Related Database Links:

BMRB 16283
PDB
DBJ BAC59214
GB AGB09412 AGQ90485 AGQ98830 AHI99009 AKU55569
REF NP_797330 WP_005461131 WP_005481834 WP_021449579 WP_025501692
SP A6B4U8