[English] 日本語
Yorodumi
- PDB-7vim: The C-terminal DNA binding domain of EsrB from Edwardsiella piscicida -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vim
TitleThe C-terminal DNA binding domain of EsrB from Edwardsiella piscicida
ComponentsProtein EsrB
KeywordsDNA BINDING PROTEIN / DNA binding / EsrB / Edwardsiella piscicida
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / 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
Similarity search - Domain/homology
Biological speciesEdwardsiella piscicida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.2 Å
AuthorsLiu, B. / Reverter, D. / Shao, S.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2015-66417-P (MINECO/FEDER) Spain
CitationJournal: To Be Published
Title: The C-terminal DNA binding domain of EsrB from Edwardsiella piscicida
Authors: Liu, B. / Reverter, D. / Shao, S.
History
DepositionSep 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein EsrB
B: Protein EsrB


Theoretical massNumber of molelcules
Total (without water)16,5572
Polymers16,5572
Non-polymers00
Water37821
1
A: Protein EsrB

B: Protein EsrB


Theoretical massNumber of molelcules
Total (without water)16,5572
Polymers16,5572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-x,y-1/2,-z-1/21
Buried area780 Å2
ΔGint-9 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.111, 58.051, 81.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Protein EsrB / Two component system response regulator


Mass: 8278.576 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Edwardsiella piscicida (bacteria) / Gene: EVK84_02890, MA13_contig00007-0127 / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A034T5T1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 12% ethanol, 5% glycerol, 100mM Tris PH 8,5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.188→47.193 Å / Num. obs: 9987 / % possible obs: 99.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 41.97 Å2 / Rpim(I) all: 0.034 / Rrim(I) all: 0.084 / Rsym value: 0.076 / Net I/av σ(I): 5.7 / Net I/σ(I): 11.4 / Num. measured all: 62270
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.19-2.316.10.6431.1829413680.2780.7020.643396.1
2.31-2.456.20.4481.5849713610.1970.490.4484.4100
2.45-2.616.50.2682.4836412830.1150.2920.2686100
2.61-2.826.20.173.9738211850.0740.1850.177.2100
2.82-3.096.40.1056.4710611030.0450.1140.10510.3100
3.09-3.466.40.0798.3646410150.0340.0860.07913.6100
3.46-3.996.20.0649.555869000.0280.070.06420.5100
3.99-4.896.20.05211.648237840.0230.0570.05225.1100
4.89-6.926.10.05311.237016090.0240.0580.05321.8100
6.92-47.1935.40.04310.420533790.020.0470.04328.699.8

-
Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.2→47.193 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2807 473 4.81 %
Rwork0.2293 9368 -
obs0.2316 9841 99.95 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.085 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso max: 99.81 Å2 / Biso mean: 43.39 Å2 / Biso min: 20.59 Å2
Baniso -1Baniso -2Baniso -3
1-2.8692 Å2-0 Å20 Å2
2---1.0262 Å20 Å2
3---3.6888 Å2
Refinement stepCycle: final / Resolution: 2.2→47.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1056 0 0 21 1077
Biso mean---41.07 -
Num. residues----131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081066
X-RAY DIFFRACTIONf_angle_d1.1121433
X-RAY DIFFRACTIONf_chiral_restr0.067171
X-RAY DIFFRACTIONf_plane_restr0.003182
X-RAY DIFFRACTIONf_dihedral_angle_d14.303425
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2-2.51840.38571570.28283040
2.5184-3.17280.2881520.22513095
3.1728-47.1930.25651640.22073233

+
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