BMRB

Biological Magnetic Resonance Data Bank


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BMRB Entry 15258

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15258
MolProbity Validation Chart

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Title: NMR solution structure of Vibrio parahaemolyticus VP2129 homodimer. Northeast Structural Genomics target VpR61.

Deposition date: 2007-05-21 Original release date: 2007-06-14

Authors: Ramelot, Theresa; Cort, John; Wang, Huang; Nwosu, Chioma; Cunningham, Kellie; Owens, Leah; Ma, Li-Chung; Xiao, Rong; Liu, Jinfeng; Baran, Michael; Swapna, G.V.T.; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano; Kennedy, Michael

Citation: Ramelot, Theresa; Cort, John; Montelione, Gaetano; Kennedy, Michael. "Solution NMR structure of Vibrio parahaemolyticus VP2129. Northeast Structural Genomics"  . ., .-..

Assembly members:
VP2129, polymer, 166 residues, 18557.6 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):
VP2129: MPITSKYTDEQVEKILAEVA LVLEKHAASPELTLMIAGNI ATNVLNQRVAASQRKLIAEK FAQALMSSLETPKTHLEHHH HHHMPITSKYTDEQVEKILA EVALVLEKHAASPELTLMIA GNIATNVLNQRVAASQRKLI AEKFAQALMSSLETPKTHLE HHHHHH

Data typeCount
13C chemical shifts348
15N chemical shifts86
1H chemical shifts587

Time Domain Data

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1subunit 11
2subunit 21

Entities:

Entity 1, subunit 1 166 residues - 18557.6 Da.

8 residues C-terminal His tag (LEHHHHHH)

1   METPROILETHRSERLYSTYRTHRASPGLU
2   GLNVALGLULYSILELEUALAGLUVALALA
3   LEUVALLEUGLULYSHISALAALASERPRO
4   GLULEUTHRLEUMETILEALAGLYASNILE
5   ALATHRASNVALLEUASNGLNARGVALALA
6   ALASERGLNARGLYSLEUILEALAGLULYS
7   PHEALAGLNALALEUMETSERSERLEUGLU
8   THRPROLYSTHRHISLEUGLUHISHISHIS
9   HISHISHISMETPROILETHRSERLYSTYR
10   THRASPGLUGLNVALGLULYSILELEUALA
11   GLUVALALALEUVALLEUGLULYSHISALA
12   ALASERPROGLULEUTHRLEUMETILEALA
13   GLYASNILEALATHRASNVALLEUASNGLN
14   ARGVALALAALASERGLNARGLYSLEUILE
15   ALAGLULYSPHEALAGLNALALEUMETSER
16   SERLEUGLUTHRPROLYSTHRHISLEUGLU
17   HISHISHISHISHISHIS

Samples:

NC_sample: VP2129, [U-13C; U-15N], 1.4 ± 0.1 mM; sodium chloride 100 ± 5 mM; calcium chloride 5 ± 0.25 mM; ammonium acetate 20 ± 1 mM; DTT 10 ± 0.5 mM; sodium azide 0.02 ± 0.001 %; H2O 95%; D2O 5%

NC5_sample: VP2129, [U-5% 13C; U-100% 15N], 1.4 ± 0.1 mM; sodium chloride 100 ± 5 mM; calcium chloride 5 ± 0.25 mM; ammonium acetate 20 ± 1 mM; DTT 10 ± 0.5 mM; sodium azide 0.02 ± 0.001 %; H2O 95%; D2O 5%

NC_in_D2O: VP2129, [U-13C; U-15N], 1.4 ± 0.1 mM; sodium chloride 100 ± 5 mM; calcium chloride 5 ± 0.25 mM; ammonium acetate 20 ± 1 mM; DTT 10 ± 0.5 mM; sodium azide 0.02 ± 0.001 %; D2O 100%

NC50_sample_in_D2O: VP2129, [U-13C; U-15N], 0.4 ± 0.1 mM; sodium chloride 100 ± 5 mM; calcium chloride 5 ± 0.25 mM; ammonium acetate 20 ± 1 mM; DTT 10 ± 0.5 mM; sodium azide 0.02 ± 0.001 %; VP2129 0.4 ± 0.1 mM; D2O 100%

sample_conditions_1: ionic strength: 0.1 M; pH: 5.5; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCNC_sampleisotropicsample_conditions_1
2D 1H-13C HSQC (aliph)NC_sampleisotropicsample_conditions_1
3D 1H-15N NOESYNC_sampleisotropicsample_conditions_1
3D 1H-13C NOESY aliphNC_sampleisotropicsample_conditions_1
3D HNCACBNC_sampleisotropicsample_conditions_1
2D 1H-13C HSQCNC5_sampleisotropicsample_conditions_1
3D 1H-13C NOESYNC_in_D2Oisotropicsample_conditions_1
4D 1H-13C NOESYNC_in_D2Oisotropicsample_conditions_1
3D HBHA(CO)NHNC_sampleisotropicsample_conditions_1
3D HNHANC_sampleisotropicsample_conditions_1
3D CBCA(CO)NHNC_sampleisotropicsample_conditions_1
3D HNCANC_sampleisotropicsample_conditions_1
3D HN(CO)CANC_sampleisotropicsample_conditions_1
3D HNCONC_sampleisotropicsample_conditions_1
3D C(CO)NHNC_sampleisotropicsample_conditions_1
3D HCCH-COSYNC_sampleisotropicsample_conditions_1
3D HCCH-TOCSYNC_sampleisotropicsample_conditions_1
2D 1H-13C HSQCNC_in_D2Oisotropicsample_conditions_1
2D 1H-15N HSQC (30 min)NC_in_D2Oisotropicsample_conditions_1
3D edited filtered 1H-13C NOESYNC50_sample_in_D2Oisotropicsample_conditions_1
3D 1H-13C NOESY aromNC_sampleisotropicsample_conditions_1
2D 1H-13C HSQC (arom ct)NC_sampleisotropicsample_conditions_1
2D 1H-13C HSQC (arom no ct)NC_sampleisotropicsample_conditions_1
2D 1H-15N HSQC (1 hr)NC_in_D2Oisotropicsample_conditions_1
2D 1H-15N HSQC (4 days)NC_in_D2Oisotropicsample_conditions_1

Software:

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

VNMR, Varian - collection

AutoStruct v2.1.1, Huang, Tejero, Powers and Montelione - data analysis

X-PLOR NIH v2.15.0, Schwieters, Kuszewski, Tjandra and Clore - structure solution

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

SPARKY v3.1, Goddard - data analysis

NMR spectrometers:

  • Varian INOVA 500 MHz
  • Varian INOVA 600 MHz
  • Varian INOVA 750 MHz

Related Database Links:

PIR PIRSF006188
SWS Q87MV2
PDB

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts