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- PDB-2l7q: Solution NMR structure of conjugate transposon protein BVU_1572(2... -

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Basic information

Entry
Database: PDB / ID: 2l7q
TitleSolution NMR structure of conjugate transposon protein BVU_1572(27-141) from Bacteroides Vulgatus, Northeast Structural Genomics Consortium Target BvR155
ComponentsConserved protein found in conjugate transposonConservation
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyConjugative transposon protein TraQ, bacteroidetes / Conjugal transfer protein TraQ superfamily / TraQ conjugal transfer protein / Uncharacterised protein PF12988, DUF3872 / Immunoglobulin-like / Sandwich / Mainly Beta / Conserved protein found in conjugate transposon
Function and homology information
Biological speciesBacteroides vulgatus (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsYang, Y. / Ramelot, T.A. / Cort, J.R. / Wang, D. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. ...Yang, Y. / Ramelot, T.A. / Cort, J.R. / Wang, D. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2012
Title: Solution NMR structure of BT_0084, a conjugative transposon lipoprotein from Bacteroides thetaiotamicron.
Authors: Ramelot, T.A. / Yang, Y. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionDec 20, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Feb 22, 2012Group: Structure summary
Revision 1.4Jan 30, 2013Group: Database references
Revision 1.5Mar 6, 2013Group: Database references
Revision 1.6Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.7May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / 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: Conserved protein found in conjugate transposon


Theoretical massNumber of molelcules
Total (without water)14,6621
Polymers14,6621
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Conserved protein found in conjugate transposon / Conservation


Mass: 14662.168 Da / Num. of mol.: 1 / Fragment: sequence database residues 27-141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / DSM 1447 / NCTC 11154 / Gene: BVU_1572 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pMGK / References: UniProt: A6L0P5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1432D 1H-15N HSQC
1532D 1H-13C HSQC
1622D 1H-13C HSQC-CT
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D HNCO
11013D HN(CA)CB
11113D CBCA(CO)NH
11213D HNCA
11313D HN(CO)CA
11413D HBHA(CO)NH
11513D H(CCO)NH
11613D C(CCO)NH
11713D (H)CCH-COSY
11813D (H)CCH-TOCSY
11933D CCH-TOCSY
12034D CC-NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.53 mM [U-100% 13C; U-100% 15N] conjugate transposon protein BVU_1572(27-141) from Bacteroides Vulgatus, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 0.02 mM sodium azide, 10 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
20.48 mM [U-5% 13C; U-100% 15N] conjugate transposon protein BVU_1572(27-141) from Bacteroides Vulgatus, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.53 mM [U-100% 13C; U-100% 15N] conjugate transposon protein BVU_1572(27-141) from Bacteroides Vulgatus, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 0.02 % sodium azide, 10 mM DTT-18, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.53 mMconjugate transposon protein BVU_1572(27-141) from Bacteroides Vulgatus-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
100 mMsodium chloride-31
5 mMcalcium chloride-41
0.02 mMsodium azide-51
10 mMDTT-61
0.48 mMconjugate transposon protein BVU_1572(27-141) from Bacteroides Vulgatus-7[U-5% 13C; U-100% 15N]2
20 mMMES-82
100 mMsodium chloride-92
5 mMcalcium chloride-102
10 mMDTT-112
0.02 mMsodium azide-122
0.53 mMconjugate transposon protein BVU_1572(27-141) from Bacteroides Vulgatus-13[U-100% 13C; U-100% 15N]3
20 mMMES-143
100 mMsodium chloride-153
5 mMcalcium chloride-163
0.02 %sodium azide-173
10 mMDTT-183
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE8502

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1.4Bruker Biospincollection
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.25Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.113Goddarddata analysis
PSVS1.4Bhattacharya and Montelionerefinement
AutoAssign2.3Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PdbStat5.1(PdbStat)-Roberto Tejero and Gaetano T. Montelionestructure solution
PINE Server1Bahrami, Markley, Assadi, and Eghbalniachemical shift autoassignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: CNS water refinement
NMR constraintsNOE constraints total: 1267 / NOE intraresidue total count: 398 / NOE long range total count: 472 / NOE medium range total count: 48 / NOE sequential total count: 349
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 20

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