[English] 日本語
Yorodumi
- PDB-7e1b: Crystal structure of VbrR-DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7e1b
TitleCrystal structure of VbrR-DNA complex
Components
  • (DNA (26-MER)) x 2
  • DNA-binding response regulator
KeywordsDNA BINDING PROTEIN / Response regulator
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-binding response regulator
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4.587 Å
AuthorsHong, S. / Zhang, X. / Zhang, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32025020, 31971120 China
CitationJournal: Acta Biochim.Biophys.Sin. / Year: 2023
Title: Structural basis of phosphorylation-induced activation of the response regulator VbrR.
Authors: Hong, S. / Guo, J. / Zhang, X. / Zhou, X. / Zhang, P. / Yu, F.
History
DepositionFeb 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-binding response regulator
B: DNA-binding response regulator
C: DNA-binding response regulator
D: DNA-binding response regulator
E: DNA-binding response regulator
F: DNA-binding response regulator
G: DNA-binding response regulator
H: DNA-binding response regulator
Y: DNA (26-MER)
Z: DNA (26-MER)
I: DNA (26-MER)
J: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)231,19612
Polymers231,19612
Non-polymers00
Water0
1
A: DNA-binding response regulator
B: DNA-binding response regulator
C: DNA-binding response regulator
D: DNA-binding response regulator
Y: DNA (26-MER)
Z: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)115,5986
Polymers115,5986
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14760 Å2
ΔGint-69 kcal/mol
Surface area48780 Å2
MethodPISA
2
E: DNA-binding response regulator
F: DNA-binding response regulator
G: DNA-binding response regulator
H: DNA-binding response regulator
I: DNA (26-MER)
J: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)115,5986
Polymers115,5986
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15150 Å2
ΔGint-70 kcal/mol
Surface area49620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)329.942, 114.064, 114.036
Angle α, β, γ (deg.)90.000, 110.020, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
DNA-binding response regulator / Response regulator / Response regulator transcription factor / Transcriptional regulator


Mass: 24906.615 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria)
Gene: C9I78_18460, CA163_10520, CGH73_12770, CGI34_20580, CGI42_14750, D5E78_24805, F0L89_03250, F0L99_22745, WR32_19050
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L8SKF9
#2: DNA chain DNA (26-MER)


Mass: 7863.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Production host: Vibrio parahaemolyticus (bacteria)
#3: DNA chain DNA (26-MER)


Mass: 8108.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Production host: Vibrio parahaemolyticus (bacteria)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.36 Å3/Da / Density % sol: 71.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaCl, 0.1 M MES pH 6.6, and 20% PEG4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97818 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97818 Å / Relative weight: 1
Reflection twinOperator: -h-k-l,l,k / Fraction: 0.45
ReflectionResolution: 4.587→50 Å / Num. obs: 15995 / % possible obs: 93.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.042 / Rrim(I) all: 0.078 / Χ2: 0.843 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
4.6-4.762.81.02416770.5340.7081.250.84872.7
4.76-4.952.90.8818290.5650.5961.0670.79679.4
4.95-5.183.20.8920410.6180.5751.0630.82688.9
5.18-5.453.30.79222840.6250.5080.9430.80898.7
5.45-5.793.30.61323030.7930.3950.7320.83199.8
5.79-6.243.20.43322760.8380.2850.520.84999.5
6.24-6.873.40.20523050.9610.130.2440.93899.7
6.87-7.863.40.10123190.9880.0640.120.9799.5
7.86-9.893.20.04223140.9970.0270.0510.93799.7
9.89-503.10.02623700.9980.0170.0320.59298.4

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 4.587→46.006 Å / Cross valid method: THROUGHOUT / σ(F): 16.35 / Phase error: 34 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3206 1657 10.36 %
Rwork0.2654 14386 -
obs0.2766 15995 71.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.28 Å2 / Biso mean: 140.2032 Å2 / Biso min: 80.24 Å2
Refinement stepCycle: final / Resolution: 4.587→46.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13328 2132 0 0 15460
Num. residues----1772
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4.6013-4.74970.3621500.321640120
4.7497-4.91920.3636560.285563132
4.9192-5.11590.329970.299380140
5.1159-5.34840.37291200.2892101150
5.3484-5.630.35191270.332116957
5.63-5.9820.38311480.3292141369
5.982-6.44270.43061890.311164082
6.4427-7.0890.40732040.2934179289
7.089-8.10990.31872040.2871181990
8.1099-10.19930.27082030.2308184790
10.1993-46.0060.26521980.2189186289

+
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