[English] 日本語
Yorodumi
- PDB-4ob4: Structure of the S. venezulae BldD DNA-binding domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ob4
TitleStructure of the S. venezulae BldD DNA-binding domain
ComponentsPutative DNA-binding protein
KeywordsDNA BINDING PROTEIN / BldD DNA binding domain / helix turn helix
Function / homology
Function and homology information


DNA-binding transcription repressor activity / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / nucleotide binding / negative regulation of DNA-templated transcription
Similarity search - Function
BldD, C-terminal / BldD-like, C-terminal domain superfamily / DNA-binding protein BldD-like, C-terminal domain / Helix-turn-helix domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) ...BldD, C-terminal / BldD-like, C-terminal domain superfamily / DNA-binding protein BldD-like, C-terminal domain / Helix-turn-helix domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
Authorsschumacher, M.A. / Tschowri, N. / Buttner, M. / Brennan, R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: Tetrameric c-di-GMP mediates effective transcription factor dimerization to control Streptomyces development.
Authors: Tschowri, N. / Schumacher, M.A. / Schlimpert, S. / Chinnam, N.B. / Findlay, K.C. / Brennan, R.G. / Buttner, M.J.
History
DepositionJan 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Structure summary
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative DNA-binding protein
B: Putative DNA-binding protein
C: Putative DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)23,6523
Polymers23,6523
Non-polymers00
Water1267
1
A: Putative DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)7,8841
Polymers7,8841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)7,8841
Polymers7,8841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)7,8841
Polymers7,8841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Putative DNA-binding protein
C: Putative DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)15,7682
Polymers15,7682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-12 kcal/mol
Surface area7400 Å2
MethodPISA
5
B: Putative DNA-binding protein

B: Putative DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)15,7682
Polymers15,7682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1150 Å2
ΔGint-11 kcal/mol
Surface area7700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.970, 79.970, 117.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Putative DNA-binding protein


Mass: 7883.973 Da / Num. of mol.: 3 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Strain: ATCC 31267 / DSM 46492 / JCM 5070 / NCIMB 12804 / NRRL 8165 / MA-4680
Gene: bldD, SAV_6861, SCO1489 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7AKQ8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 400, 0.1 M MgCl2, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2013 / Details: mirrors
RadiationMonochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→69.256 Å / Num. obs: 5897 / % possible obs: 99.9 % / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 12.4

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2EWT

2ewt


Resolution: 2.8→69.256 Å / SU ML: 0.45 / σ(F): 1.38 / Phase error: 28.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2955 590 10.01 %random
Rwork0.2297 ---
obs0.2363 5897 99.9 %-
all-5309 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.906 Å2 / ksol: 0.376 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.2029 Å2-0 Å2-0 Å2
2--9.2029 Å20 Å2
3----18.4058 Å2
Refinement stepCycle: LAST / Resolution: 2.8→69.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1617 0 0 7 1624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011641
X-RAY DIFFRACTIONf_angle_d1.1652212
X-RAY DIFFRACTIONf_dihedral_angle_d19.095622
X-RAY DIFFRACTIONf_chiral_restr0.066242
X-RAY DIFFRACTIONf_plane_restr0.005290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7999-3.08170.38261430.29831287X-RAY DIFFRACTION100
3.0817-3.52760.3071420.23311281X-RAY DIFFRACTION100
3.5276-4.44430.28651470.21211323X-RAY DIFFRACTION100
4.4443-69.27720.26911580.221416X-RAY DIFFRACTION100

+
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