[English] 日本語
Yorodumi
- PDB-1bdx: E. COLI DNA HELICASE RUVA WITH BOUND DNA HOLLIDAY JUNCTION, ALPHA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bdx
TitleE. COLI DNA HELICASE RUVA WITH BOUND DNA HOLLIDAY JUNCTION, ALPHA CARBONS AND PHOSPHATE ATOMS ONLY
Components
  • DNA (5'-D(P*GP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*C)-3')
  • HOLLIDAY JUNCTION DNA HELICASE RUVA
KeywordsTRANSFERASE/DNA / DNA-BINDING / BRANCH MIGRATION / HOLLIDAY JUNCTION / RUV / COMPLEX DNA-BINDING PROTEIN-DNA / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


Holliday junction helicase complex / Holliday junction resolvase complex / four-way junction helicase activity / SOS response / recombinational repair / four-way junction DNA binding / response to radiation / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Bacterial DNA recombination protein RuvA / Holliday junction DNA helicase RuvA, C-terminal / DNA helicase, Holliday junction RuvA type, domain I, bacterial / RuvA, C-terminal domain superfamily / RuvA N terminal domain / RuvA, C-terminal domain / RuvA domain 2-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / Holliday junction branch migration complex subunit RuvA
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, MIR / Resolution: 6 Å
AuthorsHargreaves, D. / Rice, D.W. / Sedelnikova, S.E. / Artymiuk, P.J. / Lloyd, R.G. / Rafferty, J.B.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal structure of E.coli RuvA with bound DNA Holliday junction at 6 A resolution.
Authors: Hargreaves, D. / Rice, D.W. / Sedelnikova, S.E. / Artymiuk, P.J. / Lloyd, R.G. / Rafferty, J.B.
#1: Journal: Science / Year: 1996
Title: Crystal Structure of DNA Recombination Protein Ruva and a Model for its Binding to the Holliday Junction
Authors: Rafferty, J.B. / Sedelnikova, S.E. / Hargreaves, D. / Artymiuk, P.J. / Baker, P.J. / Sharples, G.J. / Mahdi, A.A. / Lloyd, R.G. / Rice, D.W.
History
DepositionMay 11, 1998Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 9, 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
J: DNA (5'-D(P*GP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*C)-3')
K: DNA (5'-D(P*GP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*C)-3')
L: DNA (5'-D(P*GP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*C)-3')
M: DNA (5'-D(P*GP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*C)-3')
A: HOLLIDAY JUNCTION DNA HELICASE RUVA
B: HOLLIDAY JUNCTION DNA HELICASE RUVA
C: HOLLIDAY JUNCTION DNA HELICASE RUVA
D: HOLLIDAY JUNCTION DNA HELICASE RUVA


Theoretical massNumber of molelcules
Total (without water)108,0398
Polymers108,0398
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.000, 148.000, 105.600
Angle α, β, γ (deg.)90.00, 123.00, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99999, 0.00034, 0.00518), (0.00034, -0.99149, 0.13018), (0.00518, 0.13018, 0.99148)73.71131, -3.18269, 0.01618
2given(1.0E-5, -0.9977, 0.06782), (0.99804, 0.00425, 0.06249), (-0.06264, 0.06769, 0.99574)35.26724, -38.3683, 2.41632
3given(1.0E-5, 0.99804, -0.06264), (-0.9977, 0.00426, 0.06769), (0.06782, 0.0625, 0.99574)38.44391, 35.18567, -2.40027

-
Components

#1: DNA chain
DNA (5'-D(P*GP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*C)-3') / Coordinate model: P atoms only


Mass: 4898.191 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein
HOLLIDAY JUNCTION DNA HELICASE RUVA / Coordinate model: Cα atoms only


Mass: 22111.668 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Species: Escherichia coli / Strain: BL21 / Variant: DE3 / Plasmid: PAM159 / Species (production host): Escherichia coli / Gene (production host): RUVA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P0A809

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.46 Å3/Da / Density % sol: 48 %
Description: MOLECULAR REPLACEMENT PHASES WERE ONLY GOOD ENOUGH TO USE IN LOCATING HEAVY ATOMS BY DIFFERENCE FOURIER AND WERE THEN ABANDONED IN FAVOUR OF MIR PHASES.
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: PROTEIN/DNA COMPLEX WAS CRYSTALLISED FROM 0.85M SODIUM ACETATE BUFFERED WITH 100MM IMIDAZOLE AT PH 6.5, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM ACETATE11
2IMIDAZOLE11
3SODIUM ACETATE12
4IMIDAZOLE12
Crystal grow
*PLUS
Details: Hargreaves, D., (1999) Acta. Crystallogr., D55, 263.
PH range low: 7.5 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19 mg/mlprotein1drop
20.1 Mimidazole-HCl1reservoir
30.70-0.95 Msodium acetate1reservoir
41

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1997 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 5.7→17.6 Å / Num. obs: 5263 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 6.8
Reflection shellResolution: 5.7→6.01 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.224 / % possible all: 94.2
Reflection
*PLUS
% possible obs: 94 % / Num. measured all: 10906

-
Processing

Software
NameVersionClassification
CCP4model building
MLPHAREphasing
Omodel building
DENZOdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
CCP4phasing
TFFCphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, MIR
Starting model: 1CUK

1cuk


Highest resolution: 6 Å
Details: OWING TO THE LOW RESOLUTION OF THE DATA, NO POSITIONAL REFINEMENT OF THE PROTEIN RESIDUES OR DNA WAS PERFORMED
Refinement stepCycle: LAST / Highest resolution: 6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms760 64 0 0 824

+
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