[English] 日本語
Yorodumi
- PDB-6xz5: RovC - regulator of virulence interconnected with the Csr system -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xz5
TitleRovC - regulator of virulence interconnected with the Csr system
ComponentsUncharacterized protein,RovC,Uncharacterized protein
KeywordsDNA BINDING PROTEIN / transcriptional activator / type VI secretion / hexameric ring / regulator of virulence
Function / homologyDomain of unknown function DUF2285 / Domain of unknown function DUF6499 / T6SS, Transcription factor, DNA binding domain / Proteobacterial transcriptional regulator-like domain / DUF2285 domain-containing protein
Function and homology information
Biological speciesYersinia pseudotuberculosis serotype O:3
Yersinia pseudotuberculosis YPIII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsSadana, P. / Scrima, A.
CitationJournal: Plos Pathog. / Year: 2020
Title: RovC - a novel type of hexameric transcriptional activator promoting type VI secretion gene expression.
Authors: Knittel, V. / Sadana, P. / Seekircher, S. / Stolle, A.S. / Korner, B. / Volk, M. / Jeffries, C.M. / Svergun, D.I. / Heroven, A.K. / Scrima, A. / Dersch, P.
History
DepositionFeb 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein,RovC,Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6703
Polymers28,4781
Non-polymers1922
Water72140
1
A: Uncharacterized protein,RovC,Uncharacterized protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)172,01818
Polymers170,8666
Non-polymers1,15312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5
Unit cell
Length a, b, c (Å)97.278, 97.278, 46.041
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-430-

HOH

21A-439-

HOH

-
Components

#1: Protein Uncharacterized protein,RovC,Uncharacterized protein


Mass: 28477.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: An elongated stretch of ill-defined electron density is present, which corresponds to structural elements of the region 137-180. Individual amino acids could not be identified and the ...Details: An elongated stretch of ill-defined electron density is present, which corresponds to structural elements of the region 137-180. Individual amino acids could not be identified and the numbering has been assigned to 145-170 based on secondary structure prediction. Numbering in the region 145-170 may thus be not be accurate and residues are assigned as UNK.
Source: (gene. exp.) Yersinia pseudotuberculosis serotype O:3 (strain YPIII) (bacteria), (gene. exp.) Yersinia pseudotuberculosis YPIII (bacteria)
Gene: YPK_3567 / Cell line (production host): Rosetta2 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3B5N9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M KCl, 0.01 M MgSO4 , 0.01 M MES pH 5.6, 10% PEG400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.3→33.44 Å / Num. obs: 11309 / % possible obs: 99.5 % / Redundancy: 4 % / Biso Wilson estimate: 38.67 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.047 / Rrim(I) all: 0.096 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.3840.566435610950.6940.3270.6572.399.9
8.91-33.443.80.027962100.9990.0110.02321.796.2

-
Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→33.44 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0.23 / Phase error: 27.34
RfactorNum. reflection% reflection
Rfree0.2739 558 4.96 %
Rwork0.2287 --
obs0.231 11306 96.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.79 Å2 / Biso mean: 49.8864 Å2 / Biso min: 22.45 Å2
Refinement stepCycle: final / Resolution: 2.3→33.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1682 0 10 40 1732
Biso mean--64.58 45.58 -
Num. residues----214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021725
X-RAY DIFFRACTIONf_angle_d0.3722331
X-RAY DIFFRACTIONf_chiral_restr0.038250
X-RAY DIFFRACTIONf_plane_restr0.001294
X-RAY DIFFRACTIONf_dihedral_angle_d1.8131015
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3004-2.42170.31861490.2785284097
2.4217-2.57340.3441390.2761286698
2.5734-2.7720.32561590.2509271693
2.772-3.05080.25011350.2438291599
3.0508-3.49180.29281450.2265279896
3.4918-4.39770.2251470.192284997
4.3977-33.440.27741600.2313280895

+
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