[English] 日本語
Yorodumi
- PDB-6lw3: Crystal structure of RuvC from Pseudomonas aeruginosa -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lw3
TitleCrystal structure of RuvC from Pseudomonas aeruginosa
ComponentsCrossover junction endodeoxyribonuclease RuvC
KeywordsDNA BINDING PROTEIN / Holliday junction / resolvase / RuvC / Endonuclease
Function / homology
Function and homology information


crossover junction endodeoxyribonuclease / crossover junction DNA endonuclease activity / DNA recombination / nucleic acid binding / DNA repair / magnesium ion binding
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 / Crossover junction endodeoxyribonuclease RuvC
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsHu, Y. / He, Y. / Lin, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971222 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Biochemical and structural characterization of the Holliday junction resolvase RuvC from Pseudomonas aeruginosa.
Authors: Hu, Y. / He, Y. / Lin, Z.
History
DepositionFeb 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Crossover junction endodeoxyribonuclease RuvC
B: Crossover junction endodeoxyribonuclease RuvC


Theoretical massNumber of molelcules
Total (without water)34,5002
Polymers34,5002
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-19 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.379, 90.119, 61.584
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

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


Mass: 17249.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: ruvC, C0044_06995, CAZ10_11430, CGU42_02205, CKA47_33020, DY930_19340, DZ934_18445, DZ962_02435, E4V10_33000, EQH76_21345, FCG96_31605, FLI88_33360, IPC1481_05880, IPC1482_18775, IPC165_11875, ...Gene: ruvC, C0044_06995, CAZ10_11430, CGU42_02205, CKA47_33020, DY930_19340, DZ934_18445, DZ962_02435, E4V10_33000, EQH76_21345, FCG96_31605, FLI88_33360, IPC1481_05880, IPC1482_18775, IPC165_11875, IPC170_03130, IPC47_08385, IPC669_29490, RW109_RW109_05217
Production host: Escherichia coli (E. coli) / Strain (production host): DE3
References: UniProt: A0A0C7D4E1, UniProt: Q51424*PLUS, crossover junction endodeoxyribonuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 298 K / Method: evaporation
Details: 0.2 M ammonium citrate tribasic pH 7.0, 20% (w/v) polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 26012 / % possible obs: 99.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 32.84 Å2 / CC1/2: 0.995 / Net I/σ(I): 28.4
Reflection shellResolution: 2.38→2.42 Å / Num. unique obs: 1272 / CC1/2: 0.99

-
Processing

Software
NameVersionClassification
HKL-30001.13_2998data collection
HKL-30001.13_2998data scaling
PHENIXv1.13phasing
PHENIXv1.13model building
PHENIXv1.13refinement
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HJR

1hjr


Resolution: 2.38→27.11 Å / SU ML: 0.1455 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.121
RfactorNum. reflection% reflection
Rfree0.2397 652 4.7 %
Rwork0.1855 --
obs0.1882 13877 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.9 Å2
Refinement stepCycle: LAST / Resolution: 2.38→27.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2268 0 0 116 2384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00662296
X-RAY DIFFRACTIONf_angle_d0.82843100
X-RAY DIFFRACTIONf_chiral_restr0.0484370
X-RAY DIFFRACTIONf_plane_restr0.0038402
X-RAY DIFFRACTIONf_dihedral_angle_d7.51751394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.570.24151340.17942578X-RAY DIFFRACTION99.49
2.57-2.830.24571390.19552600X-RAY DIFFRACTION100
2.83-3.240.30241210.19912632X-RAY DIFFRACTION100
3.24-4.070.24341100.17542677X-RAY DIFFRACTION99.86
4.07-27.110.21451480.18532738X-RAY DIFFRACTION99.04

+
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