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- PDB-2l4w: NMR structure of the Xanthomonas VirB7 -

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Basic information

Entry
Database: PDB / ID: 2l4w
TitleNMR structure of the Xanthomonas VirB7
ComponentsUncharacterized protein
KeywordsPROTEIN TRANSPORT / Type IV secretion system / VirB7 / N0 domain / MEMBRANE PROTEIN / Xanthomonas / Lipoprotein / Bacterial outer membrane
Function / homologyPhage tail protein beta-alpha-beta fold - #70 / Toxin co-regulated pilus biosynthesis protein Q, C-terminal / Toxin co-regulated pilus biosynthesis protein Q / Phage tail protein beta-alpha-beta fold / 3-Layer(bab) Sandwich / Alpha Beta / Toxin co-regulated pilus biosynthesis protein Q C-terminal domain-containing protein
Function and homology information
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing cartesian dynamics
Model detailslowest energy, model 1
AuthorsSouza, D.P. / Farah, C.S. / Salinas, R.K.
CitationJournal: Plos Pathog. / Year: 2011
Title: A Component of the Xanthomonadaceae Type IV Secretion System Combines a VirB7 Motif with a N0 Domain Found in Outer Membrane Transport Proteins.
Authors: Souza, D.P. / Andrade, M.O. / Alvarez-Martinez, C.E. / Arantes, G.M. / Farah, C.S. / Salinas, R.K.
History
DepositionOct 15, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)12,8711
Polymers12,8711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 12871.409 Da / Num. of mol.: 1 / Fragment: VirB7-Xac2622, UNP residues 24-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: 306 / Gene: XAC2622 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RP / References: UniProt: Q8PJB3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of the VirB7 protein coded by the Xanthomonas Type IV Secretion System
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1322D 1H-1H TOCSY
1412D 1H-1H NOESY
1513D HNCO
1613D HN(CA)CO
1713D HNCA
1813D HN(CO)CA
1913D HN(CA)CB
11013D CBCA(CO)NH
11122D 1H-1H NOESY
11213D C(CO)NH
11313D HBHA(CO)NH
11413D H(CCO)NH
11523D (H)CCH-TOCSY
11613D HNHA
11713D 1H-15N NOESY
11813D 1H-15N TOCSY
11923D 1H-13C NOESY
22012D 1H-15N HSQC J-MODULATED

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2 mM [U-99% 13C; U-99% 15N] VirB7 - Xac2622-1, 10 mM [U-99% 2H] sodium acetate-2, 50 mM sodium chloride-3, 93% H2O/7% D2O93% H2O/7% D2O
20.2 mM [U-99% 13C; U-99% 15N] VirB7 - Xac2622-4, 10 mM [U-99% 2H] sodium acetate-5, 50 mM sodium chloride-6, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMVirB7 - Xac2622-1[U-99% 13C; U-99% 15N]1
10 mMsodium acetate-2[U-99% 2H]1
50 mMsodium chloride-31
0.2 mMVirB7 - Xac2622-4[U-99% 13C; U-99% 15N]2
10 mMsodium acetate-5[U-99% 2H]2
50 mMsodium chloride-62
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.065ambient 313 K
20.065ambient 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Varian INOVAVarianINOVA6002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe97.027.12.56Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisVersion 1.0. Release 15CCPNpeak picking
CcpNmr AnalysisVersion 1.0. Release 15CCPNchemical shift assignment
TALOSCornilescu, Delaglio and Baxdihedral angle prediction
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
HADDOCK2Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvinrefinement
PALES2.1Markus Zweckstetter, Ad Baxrdc data analysis
Module 22Patrice Dosset, Martin Blackledgerdc data analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics, simulated annealing cartesian dynamics
Software ordinal: 1
Details: 300 structures were calculated using the program Cyana. 50 structures with lowest target function were selected for further refinement., 50 Cyana structures were refined in explicit solvent ...Details: 300 structures were calculated using the program Cyana. 50 structures with lowest target function were selected for further refinement., 50 Cyana structures were refined in explicit solvent using the HADDOCK program. 20 lowest energy structures were selected.
NMR constraintsNOE constraints total: 2056 / NOE intraresidue total count: 438 / NOE long range total count: 663 / NOE medium range total count: 382 / NOE sequential total count: 573 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 60 / Protein psi angle constraints total count: 60
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20

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