[English] 日本語
Yorodumi
- PDB-1ixs: Structure of RuvB complexed with RuvA domain III -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ixs
TitleStructure of RuvB complexed with RuvA domain III
Components
  • Holliday junction DNA helicase ruvA
  • RuvB
KeywordsHYDROLASE / heterodimeric protein complex / AAA-ATPase domain / complex with nucleotide
Function / homology
Function and homology information


Holliday junction helicase complex / Holliday junction resolvase complex / four-way junction helicase activity / four-way junction DNA binding / DNA recombination / DNA helicase / DNA repair / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
DNA helicase, Holliday junction RuvB-type / RuvB C-terminal winged helix domain / Holliday junction DNA helicase RuvA, C-terminal / DNA helicase, Holliday junction RuvA type, domain I, bacterial / RuvA, C-terminal domain superfamily / RuvB, AAA lid domain / RuvA N terminal domain / RuvB C-terminal winged helix domain / RuvA, C-terminal domain / RuvB AAA lid domain ...DNA helicase, Holliday junction RuvB-type / RuvB C-terminal winged helix domain / Holliday junction DNA helicase RuvA, C-terminal / DNA helicase, Holliday junction RuvA type, domain I, bacterial / RuvA, C-terminal domain superfamily / RuvB, AAA lid domain / RuvA N terminal domain / RuvB C-terminal winged helix domain / RuvA, C-terminal domain / RuvB AAA lid domain / Bacterial DNA recombination protein RuvA / RuvB-like P-loop domain / Holliday junction DNA helicase RuvB P-loop domain / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 - #60 / RuvA domain 2-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Helicase, Ruva Protein; domain 3 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Holliday junction branch migration complex subunit RuvB / Holliday junction branch migration complex subunit RuvA
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsYamada, K. / Miyata, T. / Tsuchiya, D. / Oyama, T. / Fujiwara, Y. / Ohnishi, T. / Iwasaki, H. / Shinagawa, H. / Ariyoshi, M. / Mayanagi, K. / Morikawa, K.
CitationJournal: Mol.Cell / Year: 2002
Title: Crystal Structure of the RuvA-RuvB Complex: A Structural Basis for the Holliday Junction Migrating Motor Machinery
Authors: Yamada, K. / Miyata, T. / Tsuchiya, D. / Oyama, T. / Fujiwara, Y. / Ohnishi, T. / Iwasaki, H. / Shinagawa, H. / Ariyoshi, M. / Mayanagi, K. / Morikawa, K.
History
DepositionJul 4, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Holliday junction DNA helicase ruvA
B: RuvB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6233
Polymers42,1172
Non-polymers5061
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-12 kcal/mol
Surface area18220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.060, 102.060, 137.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a heterodimer in the asymmetric unit.

-
Components

#1: Protein Holliday junction DNA helicase ruvA


Mass: 6698.849 Da / Num. of mol.: 1 / Fragment: RuvA domain III
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: ruva / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9F1Q3
#2: Protein RuvB


Mass: 35417.984 Da / Num. of mol.: 1 / Fragment: residues 1-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: ruvb / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SL87, EC: 3.6.1.3
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.26 Å3/Da / Density % sol: 71.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.5 mMRuvA domain III1drop
20.5 mMRuvB1drop
31 mMAMPPNP1drop
410 mMTris-HCl1droppH8.0
50.1 M1dropNaCl
610 %(w/v)glycerol1drop
710 mMTris-HCl1reservoirpH8.0
80.1 M1reservoirNaCl
910 %(w/v)glycerol1reservoir
1010 %(w/v)PEG40001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.836 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 13, 2001
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.836 Å / Relative weight: 1
ReflectionResolution: 3.2→41 Å / Num. all: 235468 / Num. obs: 235468 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 6.8
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.1 / % possible all: 99.5
Reflection
*PLUS
Lowest resolution: 41 Å / Num. obs: 12468 / Num. measured all: 235468 / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
% possible obs: 99.5 % / Rmerge(I) obs: 0.324

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HQC

1hqc


Resolution: 3.2→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2941 633 -RANDOM
Rwork0.2313 ---
all-12434 --
obs-12434 99.1 %-
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 3.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2848 0 31 0 2879
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0073
X-RAY DIFFRACTIONc_angle_deg1.334
LS refinement shellResolution: 3.2→3.31 Å
RfactorNum. reflection% reflection
Rfree0.4718 59 -
Rwork0.35 --
obs-1209 94.3 %
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.293 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.4718 / Rfactor Rwork: 0.35

+
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://pdbjlvh1.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