[English] 日本語
Yorodumi
- PDB-7vuf: Crystal Structure of the core region of Thermus thermophilus MutS2. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vuf
TitleCrystal Structure of the core region of Thermus thermophilus MutS2.
ComponentsEndonuclease MutS2
KeywordsDNA BINDING PROTEIN / ATPase / hydrolase
Function / homology
Function and homology information


mismatched DNA binding / negative regulation of DNA recombination / mismatch repair / endonuclease activity / Hydrolases; Acting on ester bonds / ATP hydrolysis activity / ATP binding
Similarity search - Function
MutS2 and Smr-associated SH3 domain / MutS2 and Smr-associated SH3 domain / Endonuclease MutS2 / Smr domain superfamily / Smr domain / Small MutS-related domain / Smr domain / Smr domain profile. / DNA mismatch repair protein MutS, C-terminal / DNA mismatch repair protein MutS, core ...MutS2 and Smr-associated SH3 domain / MutS2 and Smr-associated SH3 domain / Endonuclease MutS2 / Smr domain superfamily / Smr domain / Small MutS-related domain / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Endonuclease MutS2
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsFukui, K. / Yano, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2022
Title: Structural and functional insights into the mechanism by which MutS2 recognizes a DNA junction.
Authors: Fukui, K. / Inoue, M. / Murakawa, T. / Baba, S. / Kumasaka, T. / Yano, T.
History
DepositionNov 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Endonuclease MutS2
A: Endonuclease MutS2
C: Endonuclease MutS2
D: Endonuclease MutS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,48912
Polymers216,7214
Non-polymers7678
Water1,928107
1
B: Endonuclease MutS2
hetero molecules

C: Endonuclease MutS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9168
Polymers108,3612
Non-polymers5556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area3910 Å2
ΔGint-30 kcal/mol
Surface area43730 Å2
MethodPISA
2
A: Endonuclease MutS2
D: Endonuclease MutS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,5734
Polymers108,3612
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-31 kcal/mol
Surface area43060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.485, 114.207, 292.879
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
Endonuclease MutS2


Mass: 54180.355 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: No clear electron density was observed for the residues 166-172, 187-196, 361-367, and 488 of the chain A, 1, 167-171, 187-196, 361-367, and 487-488 of the chain B, 164-170, 361-365, 467, ...Details: No clear electron density was observed for the residues 166-172, 187-196, 361-367, and 488 of the chain A, 1, 167-171, 187-196, 361-367, and 487-488 of the chain B, 164-170, 361-365, 467, 487-488 of the chain C, 1, 167-173, 192-195, 211-218, 360-364 of the chain D.
Source: (gene. exp.) Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (bacteria)
Strain: ATCC 27634 / DSM 579 / HB8 / Gene: mutS2, TTHA1645 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: Q5SHT5, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 66.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25 mM HEPES-NaOH (pH 7.0), 100 mM potassium chloride, 12.5 mM magnesium sulfate, 10% (v/v) PEG 200

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 53869 / % possible obs: 99.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.271 / Rpim(I) all: 0.117 / Rrim(I) all: 0.296 / Χ2: 2.009 / Net I/σ(I): 10.13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-3.146.51.671111110.4990.711.8181.246100
3.14-3.396.40.899111360.7120.3830.9791.346100
3.39-3.736.40.515111430.8750.2210.5611.654100
3.73-4.266.40.319112300.9190.1380.3482.46100
4.26-5.376.30.217112980.9260.0950.2373.908100
5.37-106.30.166117110.9460.070.18114.51399.8

-
Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
PHENIX1.19.2model building
Coot0.7.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→40.89 Å / SU ML: 0.4461 / Cross valid method: FREE R-VALUE / σ(F): 0.13 / Phase error: 27.436
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2785 2586 4.8 %
Rwork0.2248 51283 -
obs0.2274 53869 94.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.5 Å2
Refinement stepCycle: LAST / Resolution: 3.11→40.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14285 0 50 107 14442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001814525
X-RAY DIFFRACTIONf_angle_d0.503519607
X-RAY DIFFRACTIONf_chiral_restr0.03612276
X-RAY DIFFRACTIONf_plane_restr0.00362568
X-RAY DIFFRACTIONf_dihedral_angle_d13.99223701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.170.40231150.3112499X-RAY DIFFRACTION83.41
3.17-3.230.35611270.30032559X-RAY DIFFRACTION85.95
3.23-3.30.39131410.28892640X-RAY DIFFRACTION89.34
3.3-3.380.37871260.27312766X-RAY DIFFRACTION91.06
3.38-3.470.32821380.25762752X-RAY DIFFRACTION91.95
3.47-3.560.33711390.25222709X-RAY DIFFRACTION91.72
3.56-3.660.25191540.23012824X-RAY DIFFRACTION94
3.66-3.780.29691440.22972826X-RAY DIFFRACTION93.75
3.78-3.920.26931360.21712837X-RAY DIFFRACTION94.65
3.92-4.070.24881470.21162864X-RAY DIFFRACTION94.66
4.07-4.260.23461490.19712882X-RAY DIFFRACTION95.95
4.26-4.480.27951540.19062916X-RAY DIFFRACTION96.66
4.48-4.760.24871320.19412954X-RAY DIFFRACTION96.83
4.76-5.130.28891480.19982946X-RAY DIFFRACTION97.48
5.13-5.650.25151690.22792954X-RAY DIFFRACTION97.56
5.65-6.460.2931490.25143021X-RAY DIFFRACTION98.17
6.46-8.130.26031710.21433092X-RAY DIFFRACTION99.6
8.13-100.22421470.20143242X-RAY DIFFRACTION99.24
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.12378732089-0.1611321022430.5917481926280.151216459652-0.1253435857350.558885481738-0.0571225634287-0.1358865993660.138806570118-0.0794845189133-0.0108556719864-0.0915441463243-0.0220891301551-0.1116889991180.07272602599630.374336356414-0.02307236513640.03084486809980.299201155789-0.09183213024950.396178048841-0.613484000106-13.8303376579-40.1621527154
21.14438087159-0.1230833142910.3884728928770.171719693455-0.1779177966970.2282794931460.0506299779061-0.0877007423893-0.149818121956-0.00062486390312-0.0109679541056-0.0208997353785-0.0283784153164-0.0196663571264-0.03024098469150.3791650106910.001652993294610.03300748497810.309444488069-0.1134567565330.318950119994-29.395196803815.0533148506-20.7364899565
31.22888052735-1.020383390220.5905527027080.957470581246-0.3967599659760.2871279790240.06791246606120.0106436305151-0.0395935883882-0.0702796830793-0.05999697999650.08672502091680.053357924854-0.0076426082952-0.0001652726633190.332638164363-0.03810874377730.04906184759750.3990173863240.007999568967510.298715360864-14.443367292653.8405114075-60.0481900348
40.862064456046-0.5735303415880.1663098614030.495317195662-0.1788364134520.02012897741880.01307690223360.1213426853480.127568097836-0.0483259295661-0.0570829127937-0.1488813724320.0500982129355-0.01869162016490.03430962765610.45613169015-0.02473163291570.02390159843030.397616307546-0.09202215001960.375980663682-10.016380643463.0887819961-9.91392433066
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain B and resseq 2:487)BA2 - 4871 - 471
22(chain A and resseq 1:485)AB1 - 4851 - 461
33(chain C and resseq 1:486)CC1 - 4861 - 473
44(chain D and resseq 2:488)DD2 - 4881 - 463

+
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://pdbjlc1.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