[English] 日本語
Yorodumi
- PDB-4ld0: T. thermophilus RuvC in complex with Holliday junction substrate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ld0
TitleT. thermophilus RuvC in complex with Holliday junction substrate
Components
  • Crossover junction endodeoxyribonuclease RuvC
  • DNA 11-MER
  • DNA 13-MER
  • DNA 31-MER
KeywordsHYDROLASE/DNA / RNase H fold / nuclease / DNA / HYDROLASE-DNA complex
Function / homology
Function and homology information


crossover junction endodeoxyribonuclease / Holliday junction resolvase complex / crossover junction DNA endonuclease activity / DNA recombination / DNA repair / magnesium ion binding / DNA binding / cytoplasm
Similarity search - Function
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
DNA / DNA (> 10) / Crossover junction endodeoxyribonuclease RuvC
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.75 Å
AuthorsGorecka, K.M. / Komorowska, W. / Nowotny, M.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Crystal structure of RuvC resolvase in complex with Holliday junction substrate.
Authors: Gorecka, K.M. / Komorowska, W. / Nowotny, M.
History
DepositionJun 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Dec 4, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Crossover junction endodeoxyribonuclease RuvC
B: Crossover junction endodeoxyribonuclease RuvC
C: DNA 31-MER
D: DNA 13-MER
F: DNA 11-MER


Theoretical massNumber of molelcules
Total (without water)52,9655
Polymers52,9655
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-62 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.356, 106.356, 132.653
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 11:20 or resseq 28:71 or resseq...
21chain B and (resseq 11:20 or resseq 28:71 or resseq...
12chain A and (resseq 1:20 or resseq 26:115 or resseq 122:165 )
22chain B and (resseq 1:20 or resseq 26:115 or resseq 122:165 )

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRVALVALchain 'A' and (resseq 11:20 or resseq 28:71 or resseq...AA11 - 2014 - 23
121ALAALAGLUGLUchain 'A' and (resseq 11:20 or resseq 28:71 or resseq...AA28 - 7131 - 74
131LEULEUALAALAchain 'A' and (resseq 11:20 or resseq 28:71 or resseq...AA80 - 11583 - 118
141GLUGLULYSLYSchain 'A' and (resseq 11:20 or resseq 28:71 or resseq...AA123 - 136126 - 139
151ARGARGMETMETchain 'A' and (resseq 11:20 or resseq 28:71 or resseq...AA140 - 160143 - 163
211THRTHRVALVALchain 'B' and (resseq 11:20 or resseq 28:71 or resseq...BB11 - 2014 - 23
221ALAALAGLUGLUchain 'B' and (resseq 11:20 or resseq 28:71 or resseq...BB28 - 7131 - 74
231LEULEUALAALAchain 'B' and (resseq 11:20 or resseq 28:71 or resseq...BB80 - 11583 - 118
241GLUGLULYSLYSchain 'B' and (resseq 11:20 or resseq 28:71 or resseq...BB123 - 136126 - 139
251ARGARGMETMETchain 'B' and (resseq 11:20 or resseq 28:71 or resseq...BB140 - 160143 - 163
112METMETVALVALchain 'A' and (resseq 1:20 or resseq 26:115 or resseq 122:165 )AA1 - 204 - 23
122LEULEUALAALAchain 'A' and (resseq 1:20 or resseq 26:115 or resseq 122:165 )AA26 - 11529 - 118
132LYSLYSPROPROchain 'A' and (resseq 1:20 or resseq 26:115 or resseq 122:165 )AA122 - 165125 - 168
212METMETVALVALchain 'B' and (resseq 1:20 or resseq 26:115 or resseq 122:165 )BB1 - 204 - 23
222LEULEUALAALAchain 'B' and (resseq 1:20 or resseq 26:115 or resseq 122:165 )BB26 - 11529 - 118
232LYSLYSPROPROchain 'B' and (resseq 1:20 or resseq 26:115 or resseq 122:165 )BB122 - 165125 - 168

NCS ensembles :
ID
1
2

-
Components

#1: Protein Crossover junction endodeoxyribonuclease RuvC / Holliday junction nuclease RuvC / Holliday junction resolvase RuvC


Mass: 18073.135 Da / Num. of mol.: 2 / Fragment: RuvC / Mutation: E70Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: ruvC, TTHA1090 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SJC4, crossover junction endodeoxyribonuclease
#2: DNA chain DNA 31-MER


Mass: 9519.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA
#3: DNA chain DNA 13-MER


Mass: 3917.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA
#4: DNA chain DNA 11-MER


Mass: 3382.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.09 Å3/Da / Density % sol: 69.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.3-0.5 M ammonium phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 24, 2009
RadiationMonochromator: horizontally side diffracting Silicon 111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. all: 9622 / Num. obs: 9622 / % possible obs: 99.5 % / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 2.2
Reflection shellResolution: 3.7→3.96 Å / % possible all: 97.7

-
Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.75→46.053 Å / SU ML: 0.55 / σ(F): 2.02 / Phase error: 38.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3293 464 5.01 %
Rwork0.2668 --
obs0.2699 9255 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.75→46.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 1118 0 0 3361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173586
X-RAY DIFFRACTIONf_angle_d1.9525026
X-RAY DIFFRACTIONf_dihedral_angle_d25.3061333
X-RAY DIFFRACTIONf_chiral_restr0.089584
X-RAY DIFFRACTIONf_plane_restr0.01457
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A874X-RAY DIFFRACTIONTORSIONAL0.095
12B874X-RAY DIFFRACTIONTORSIONAL0.095
21A1054X-RAY DIFFRACTIONTORSIONAL0.095
22B1054X-RAY DIFFRACTIONTORSIONAL0.095
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7509-4.29330.32051510.27522871X-RAY DIFFRACTION100
4.2933-5.40780.361540.3022910X-RAY DIFFRACTION100
5.4078-46.05690.31921590.24963010X-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://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