[English] 日本語
Yorodumi
- PDB-8h1f: Aquifex aeolicus MutL endonuclease domain complexed with zinc ion... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8h1f
TitleAquifex aeolicus MutL endonuclease domain complexed with zinc ions after soaking
ComponentsDNA mismatch repair protein MutL
KeywordsDNA BINDING PROTEIN / endonuclease
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 VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.22 Å
AuthorsFukui, K. / Yano, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K07376 Japan
CitationJournal: Life Sci Alliance / Year: 2023
Title: Catalytic mechanism of the zinc-dependent MutL endonuclease reaction.
Authors: Fukui, K. / Yamamoto, T. / Murakawa, T. / Baba, S. / Kumasaka, T. / Yano, T.
History
DepositionOct 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA mismatch repair protein MutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,99811
Polymers12,3521
Non-polymers64610
Water2,198122
1
A: DNA mismatch repair protein MutL
hetero molecules

A: DNA mismatch repair protein MutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,99622
Polymers24,7052
Non-polymers1,29120
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4600 Å2
ΔGint-331 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.529, 35.529, 167.288
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein DNA mismatch repair protein MutL /


Mass: 12352.259 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Strain: VF5 / Gene: mutL / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: O67518
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 200 mM sodium acetate (pH 4.6), 100 mM CdCl2, and 30 % (v/v) polyethylene glycol 300

-
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: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.22→34.75 Å / Num. obs: 33167 / % possible obs: 99.7 % / Redundancy: 13.4 % / Biso Wilson estimate: 12.99 Å2 / CC1/2: 0.91 / Rpim(I) all: 0.02 / Net I/σ(I): 57.2
Reflection shellResolution: 1.22→1.26 Å / Mean I/σ(I) obs: 4.2 / Num. unique obs: 3220 / CC1/2: 0.93 / Rpim(I) all: 0.17

-
Processing

Software
NameVersionClassification
PRIME-X1.19.2-4158refinement
PHENIX1.19.2-4158model building
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
Coot0.7.2model building
RefinementMethod to determine structure: SAD / Resolution: 1.22→34.75 Å / SU ML: 0.1027 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.1003
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1754 2000 6.03 %
Rwork0.1572 31167 -
obs0.1583 33167 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.7 Å2
Refinement stepCycle: LAST / Resolution: 1.22→34.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms847 0 22 122 991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061878
X-RAY DIFFRACTIONf_angle_d0.86611179
X-RAY DIFFRACTIONf_chiral_restr0.072126
X-RAY DIFFRACTIONf_plane_restr0.0085148
X-RAY DIFFRACTIONf_dihedral_angle_d14.9823344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.250.25371370.192130X-RAY DIFFRACTION99.3
1.25-1.280.23251390.14822182X-RAY DIFFRACTION99.49
1.28-1.320.14391410.13182185X-RAY DIFFRACTION99.61
1.32-1.360.17681390.13342173X-RAY DIFFRACTION99.7
1.36-1.410.15951390.13772164X-RAY DIFFRACTION99.87
1.41-1.470.17311430.11982217X-RAY DIFFRACTION99.96
1.47-1.540.14731390.11532174X-RAY DIFFRACTION100
1.54-1.620.14431430.11682232X-RAY DIFFRACTION99.96
1.62-1.720.14061400.12782186X-RAY DIFFRACTION100
1.72-1.850.1561440.13992248X-RAY DIFFRACTION100
1.85-2.040.18411450.13972233X-RAY DIFFRACTION100
2.04-2.330.17791450.1512269X-RAY DIFFRACTION100
2.33-2.940.18371480.18262319X-RAY DIFFRACTION100
2.94-100.19591580.18382455X-RAY DIFFRACTION99.24

+
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