[English] 日本語
Yorodumi
- PDB-5x9y: Crystal structure of the ATPase domain from bacterial mismatch re... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5x9y
TitleCrystal structure of the ATPase domain from bacterial mismatch repair endonuclease Aquifex aeolicus MutL.
ComponentsDNA mismatch repair protein MutL
KeywordsDNA BINDING PROTEIN / MutL / DNA mismatch repair / endonuclease / ATPase
Function / homology
Function and homology information


mismatch repair complex / mismatched DNA binding / ATP-dependent DNA damage sensor activity / mismatch repair / ATP hydrolysis activity / ATP binding
Similarity search - Function
DNA mismatch repair protein, MutL / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site / DNA mismatch repair protein MutL/Mlh/Pms / DNA mismatch repair protein, C-terminal domain ...DNA mismatch repair protein, MutL / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site / DNA mismatch repair protein MutL/Mlh/Pms / DNA mismatch repair protein, C-terminal domain / DNA mismatch repair proteins mutL / hexB / PMS1 signature. / DNA mismatch repair protein, C-terminal domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / DNA mismatch repair protein MutL
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.443 Å
AuthorsFukui, K. / Yano, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)16K18680 Japan
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Crystal structure and DNA-binding property of the ATPase domain of bacterial mismatch repair endonuclease MutL from Aquifex aeolicus
Authors: Fukui, K. / Iino, H. / Baba, S. / Kumasaka, T. / Kuramitsu, S. / Yano, T.
History
DepositionMar 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: DNA mismatch repair protein MutL
A: DNA mismatch repair protein MutL
B: DNA mismatch repair protein MutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,2035
Polymers106,9903
Non-polymers2122
Water34219
1
C: DNA mismatch repair protein MutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7702
Polymers35,6631
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DNA mismatch repair protein MutL


Theoretical massNumber of molelcules
Total (without water)35,6631
Polymers35,6631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: DNA mismatch repair protein MutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7702
Polymers35,6631
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.929, 145.253, 176.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
DetailsTHE BIOLOGICAL ASSEMBLY WAS EXPERIMENTALLY CONFIRMED BY SAXS AND GEL FILTRATION ANALYSES.

-
Components

#1: Protein DNA mismatch repair protein MutL /


Mass: 35663.422 Da / Num. of mol.: 3 / Fragment: UNP residues 9-315
Source method: isolated from a genetically manipulated source
Details: Residues 1-11, 41-43, 66-91, 187-190, 273-282, and 302-308 of chain A-C are disordered in the crystal structure.
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: mutL, aq_1578 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: O67518
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.84 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 50 mM Bis-Tris 1.5 M sodium chloride 25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.44→43.05 Å / Num. obs: 21839 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.054 / Net I/σ(I): 16.3
Reflection shellResolution: 3.44→3.57 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.008 / Mean I/σ(I) obs: 2.13 / Num. unique obs: 1053 / CC1/2: 0.725 / Rpim(I) all: 0.397 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
PHENIXmodel building
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BKN
Resolution: 3.443→43.05 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.95
RfactorNum. reflection% reflection
Rfree0.2954 1869 9.16 %
Rwork0.2561 --
obs0.2597 20395 92.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.443→43.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6108 0 14 19 6141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026198
X-RAY DIFFRACTIONf_angle_d0.5878284
X-RAY DIFFRACTIONf_dihedral_angle_d13.7143143
X-RAY DIFFRACTIONf_chiral_restr0.043945
X-RAY DIFFRACTIONf_plane_restr0.0041044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.443-3.5360.36571160.31471150X-RAY DIFFRACTION77
3.536-3.640.34671350.29151328X-RAY DIFFRACTION87
3.64-3.75740.30651340.28811311X-RAY DIFFRACTION87
3.7574-3.89160.32191350.29281318X-RAY DIFFRACTION88
3.8916-4.04730.31631300.27391402X-RAY DIFFRACTION91
4.0473-4.23140.31311490.25561427X-RAY DIFFRACTION93
4.2314-4.45430.27511470.22831456X-RAY DIFFRACTION97
4.4543-4.73310.24121490.22541456X-RAY DIFFRACTION95
4.7331-5.0980.24811470.22151489X-RAY DIFFRACTION97
5.098-5.61010.29341530.26011498X-RAY DIFFRACTION98
5.6101-6.41980.30191530.25891522X-RAY DIFFRACTION98
6.4198-8.08020.28581580.27661548X-RAY DIFFRACTION99
8.0802-43.050.30861630.24541621X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -18.7732 Å / Origin y: 19.4752 Å / Origin z: 18.967 Å
111213212223313233
T0.7284 Å2-0.0223 Å2-0.0326 Å2-0.7003 Å20.0343 Å2--0.864 Å2
L0.8389 °20.1452 °20.9528 °2-0.6775 °20.4977 °2--2.4077 °2
S0.143 Å °0.1771 Å °0.1464 Å °-0.1079 Å °-0.2143 Å °0.3116 Å °0.1354 Å °-0.3942 Å °0.0677 Å °
Refinement TLS groupSelection details: all

+
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