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- PDB-2jpq: Solution NMR structure of homodimer VP2129 from Vibrio parahaemol... -

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Basic information

Entry
Database: PDB / ID: 2jpq
TitleSolution NMR structure of homodimer VP2129 from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium target VpR61.
ComponentsUPF0352 protein VP2129
KeywordsSTRUCTURAL GENOMICS / dimer / all alpha / homodimer / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyUncharacterised protein family UPF0352 / YejL-like superfamily / Protein of unknown function (DUF1414) / YejL-like / YejL-like / Orthogonal Bundle / Mainly Alpha / UPF0352 protein VP2129
Function and homology information
Biological speciesVibrio parahaemolyticus (bacteria)
MethodSOLUTION NMR / distance geometry, simulated annealing
Model detailshomodimer. All helical. Domain swapped dimer.
AuthorsRamelot, T.A. / Cort, J.R. / Wang, H. / Nwosu, C. / Cunningham, K. / Owens, L. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. ...Ramelot, T.A. / Cort, J.R. / Wang, H. / Nwosu, C. / Cunningham, K. / Owens, L. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of Vibrio parahaemolyticus VP2129. Northeast Structural Genomics
Authors: Ramelot, T.A. / Cort, J.R. / Montelione, G.A. / Kennedy, M.A.
History
DepositionMay 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.6May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0352 protein VP2129
B: UPF0352 protein VP2129


Theoretical massNumber of molelcules
Total (without water)18,5692
Polymers18,5692
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein UPF0352 protein VP2129


Mass: 9284.696 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: VP2129 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pMGK / References: UniProt: Q87MV2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: homodimer. All helical. domain swapped dimer.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-15N NOESY
1413D 1H-13C NOESY aliph
1513D HN(CA)CB
1622D 1H-13C HSQC
1733D 1H-13C NOESY
1834D 1H-13C NOESY
1913D HBHA(CO)NH
11013D HNHA
11113D CBCA(CO)NH
11213D HNCA
11313D HN(CO)CA
11413D HNCO
11513D C(CO)NH
11613D (H)CCH-COSY
11713D (H)CCH-TOCSY
11832D 1H-13C HSQC
11932D 1H-15N HSQC
12043D edited filtered 1H-13C NOESY
12113D 1H-13C NOESY arom

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Sample preparation

Details
Solution-IDContentsSolvent system
11.4 mM [U-13C; U-15N] VP2129, 100 mM sodium chloride, 5 mM calcium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
21.4 mM [U-5% 13C; U-100% 15N] VP2129, 100 mM sodium chloride, 5 mM calcium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
31.4 mM [U-13C; U-15N] VP2129, 100 mM sodium chloride, 5 mM calcium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % sodium azide, 100% D2O100% D2O
40.4 mM [U-13C; U-15N] VP2129, 100 mM sodium chloride, 5 mM calcium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % sodium azide, 0.4 mM VP2129, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.4 mMVP2129[U-13C; U-15N]1
100 mMsodium chloride1
5 mMcalcium chloride1
20 mMammonium acetate1
10 mMDTT1
0.02 %sodium azide1
1.4 mMVP2129[U-5% 13C; U-100% 15N]2
100 mMsodium chloride2
5 mMcalcium chloride2
20 mMammonium acetate2
10 mMDTT2
0.02 %sodium azide2
1.4 mMVP2129[U-13C; U-15N]3
100 mMsodium chloride3
5 mMcalcium chloride3
20 mMammonium acetate3
10 mMDTT3
0.02 %sodium azide3
0.4 mMVP2129-1[U-13C; U-15N]4
100 mMsodium chloride4
5 mMcalcium chloride4
20 mMammonium acetate4
10 mMDTT4
0.02 %sodium azide4
0.4 mMVP2129-24
Sample conditionsIonic strength: 0.1 / pH: 5.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipenmrpipe_linuxDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMRVariancollection
AutoStructure2.1.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.15.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.1Goddarddata analysis
AutoAssign2.3.0structure solution
CNS1.1structure solution
PSVS1.3structure solution
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1476 / NOE intraresidue total count: 0 / NOE long range total count: 404 / NOE medium range total count: 820 / NOE sequential total count: 252 / Hydrogen bond constraints total count: 3 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 100 / Protein psi angle constraints total count: 100
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.02 Å / Maximum torsion angle constraint violation: 0.04 ° / Maximum upper distance constraint violation: 0.04 Å
NMR ensemble rmsDistance rms dev: 0.002 Å

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