[English] 日本語
Yorodumi
- PDB-4od6: Structure of Smr domain of MutS2 from Deinococcus radiodurans, Mn... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4od6
TitleStructure of Smr domain of MutS2 from Deinococcus radiodurans, Mn2+ soaked
ComponentsEndonuclease MutS2
KeywordsHYDROLASE / nuclease / Mn2+
Function / homology
Function and homology information


mismatched DNA binding / negative regulation of DNA recombination / mismatch repair / double-stranded DNA binding / endonuclease activity / Hydrolases; Acting on ester bonds / ATP hydrolysis activity / ATP binding
Similarity search - Function
Ribosomal Protein S8; Chain: A, domain 1 - #110 / : / Endonuclease MutS2 / MutS2 and Smr-associated SH3 domain / MutS2 and Smr-associated SH3 domain / Smr domain / Small MutS-related domain / Smr domain superfamily / Smr domain / Smr domain profile. ...Ribosomal Protein S8; Chain: A, domain 1 - #110 / : / Endonuclease MutS2 / MutS2 and Smr-associated SH3 domain / MutS2 and Smr-associated SH3 domain / Smr domain / Small MutS-related domain / Smr domain superfamily / Smr domain / Smr domain profile. / DNA mismatch repair protein MutS, C-terminal / DNA mismatch repair protein MutS, core / DNA mismatch repair protein MutS, core domain superfamily / MutS domain V / DNA mismatch repair proteins mutS family signature. / DNA-binding domain of DNA mismatch repair MUTS family / ATPase domain of DNA mismatch repair MUTS family / Ribosomal Protein S8; Chain: A, domain 1 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.199 Å
AuthorsZhang, H. / Zhao, Y. / Xu, Q. / Hua, Y.J.
CitationJournal: Dna Repair / Year: 2014
Title: Structural and functional studies of MutS2 from Deinococcus radiodurans.
Authors: Zhang, H. / Xu, Q. / Lu, M. / Xu, X. / Wang, Y. / Wang, L. / Zhao, Y. / Hua, Y.
History
DepositionJan 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endonuclease MutS2


Theoretical massNumber of molelcules
Total (without water)9,8651
Polymers9,8651
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.120, 46.640, 49.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Endonuclease MutS2


Mass: 9865.203 Da / Num. of mol.: 1 / Fragment: Smr domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: mutS2, DR_1976 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9RSZ3, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 1.81 Å3/Da / Density % sol: 32.11 %
Crystal growTemperature: 297 K
Method: crystal formed spontaneously in protein solution stored at 4 degree
pH: 8.8
Details: 30mM NaCl and 20mM Tris-HCl, soaked in 5mM MnCl2 before x-ray data collection, pH 8.8, crystal formed spontaneously in protein solution stored at 4 degree, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2011
RadiationMonochromator: silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.199→30 Å / Num. all: 23113 / Num. obs: 22713 / % possible obs: 98.3 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.199→1.23 Å / % possible all: 96.7

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.199→26.31 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 22.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2089 1170 5.16 %Random
Rwork0.1821 ---
obs0.1834 22694 98.17 %-
all-23117 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.199→26.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms635 0 0 119 754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019694
X-RAY DIFFRACTIONf_angle_d1.849937
X-RAY DIFFRACTIONf_dihedral_angle_d13.04273
X-RAY DIFFRACTIONf_chiral_restr0.093104
X-RAY DIFFRACTIONf_plane_restr0.011127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.199-1.25350.361620.2892592X-RAY DIFFRACTION98
1.2535-1.31960.28621560.25652659X-RAY DIFFRACTION99
1.3196-1.40230.2191320.18092729X-RAY DIFFRACTION100
1.4023-1.51060.24451410.18582705X-RAY DIFFRACTION99
1.5106-1.66260.18071500.15032703X-RAY DIFFRACTION100
1.6626-1.90310.18031320.15952716X-RAY DIFFRACTION99
1.9031-2.39740.19261420.1822651X-RAY DIFFRACTION95
2.3974-26.31590.18381550.17012769X-RAY DIFFRACTION96

+
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