[English] 日本語
Yorodumi
- PDB-1hjr: ATOMIC STRUCTURE OF THE RUVC RESOLVASE: A HOLLIDAY JUNCTION-SPECI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hjr
TitleATOMIC STRUCTURE OF THE RUVC RESOLVASE: A HOLLIDAY JUNCTION-SPECIFIC ENDONUCLEASE FROM E. COLI
ComponentsHOLLIDAY JUNCTION RESOLVASE (RUVC)
KeywordsSITE-SPECIFIC RECOMBINASE
Function / homology
Function and homology information


crossover junction endodeoxyribonuclease / Holliday junction resolvase complex / crossover junction DNA endonuclease activity / recombinational repair / response to radiation / nucleic acid binding / magnesium ion binding / cytoplasm
Similarity search - Function
Crossover junction endodeoxyribonuclease RuvC, magnesium-binding site / Crossover junction endodeoxyribonuclease ruvC signature. / Crossover junction endodeoxyribonuclease RuvC / Crossover junction endodeoxyribonuclease RuvC / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Crossover junction endodeoxyribonuclease RuvC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsAriyoshi, M. / Vassylyev, D.G. / Morikawa, K.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1994
Title: Atomic structure of the RuvC resolvase: a holliday junction-specific endonuclease from E. coli.
Authors: Ariyoshi, M. / Vassylyev, D.G. / Iwasaki, H. / Nakamura, H. / Shinagawa, H. / Morikawa, K.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Preliminary Crystallographic Study of Escherichia Coli RuvC Protein: An Endonuclease Specific for Holliday Junctions
Authors: Ariyoshi, M. / Vassylyev, D.G. / Iwasaki, H. / Fujishima, A. / Shinagawa, H. / Morikawa, K.
History
DepositionDec 2, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HOLLIDAY JUNCTION RESOLVASE (RUVC)
B: HOLLIDAY JUNCTION RESOLVASE (RUVC)
C: HOLLIDAY JUNCTION RESOLVASE (RUVC)
D: HOLLIDAY JUNCTION RESOLVASE (RUVC)


Theoretical massNumber of molelcules
Total (without water)67,9704
Polymers67,9704
Non-polymers00
Water3,567198
1
A: HOLLIDAY JUNCTION RESOLVASE (RUVC)
C: HOLLIDAY JUNCTION RESOLVASE (RUVC)


Theoretical massNumber of molelcules
Total (without water)33,9852
Polymers33,9852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-17 kcal/mol
Surface area15910 Å2
MethodPISA
2
B: HOLLIDAY JUNCTION RESOLVASE (RUVC)
D: HOLLIDAY JUNCTION RESOLVASE (RUVC)


Theoretical massNumber of molelcules
Total (without water)33,9852
Polymers33,9852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-17 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.800, 139.600, 32.400
Angle α, β, γ (deg.)90.00, 93.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9997, 0.01319, -0.0204), (-0.0138, -0.9994, 0.0321), (-0.0199, 0.03234, 0.9993)35.73, -9.35, -16.11
2given(-0.4791, 0.3792, 0.7917), (0.2988, -0.7776, 0.5533), (0.8254, 0.5016, 0.2592)-23.38, 22.64, 5.93
3given(0.4891, -0.3552, 0.7966), (-0.2994, 0.7895, 0.5358), (-0.8192, -0.5006, 0.2798)-57.46, 31.06, 24.55

-
Components

#1: Protein
HOLLIDAY JUNCTION RESOLVASE (RUVC)


Mass: 16992.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
References: UniProt: P0A814, crossover junction endodeoxyribonuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal grow
*PLUS
Method: microdialysis / Details: Ariyoshi, M., (1994) J.Mol.Biol., 241, 281.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18.0 mg/mlprotein solution11
250 mMTris-HCl12
3300-400 mM12NaCl
47.5 %(v/v)glycerol12
51 mMEDTA12
61 mMDTT12

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 15545

-
Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→6 Å / Rfactor Rwork: 0.157 / Rfactor obs: 0.157
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4768 0 0 198 4966
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Num. reflection obs: 15545 / Rfactor obs: 0.157 / Rfactor Rwork: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 0.039

+
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