[English] 日本語
Yorodumi
- PDB-2l4w: NMR structure of the Xanthomonas VirB7 -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)12,8711
Polymers12,8711
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 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

-
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

-
Experimental details

-
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

-
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)
10.06 5.0 ambient 313 K
20.06 5.0 ambient 303 K

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more