[English] 日本語
Yorodumi
- PDB-3u6m: Structural effects of sequence context on lesion recognition by MutM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3u6m
TitleStructural effects of sequence context on lesion recognition by MutM
Components
  • DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*AP*GP*GP*AP*CP*GP*C)-3')
  • DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*TP*(8OG)P*GP*TP*(CX2)P*TP*AP*CP*C)-3')
  • Formamidopyrimidine-DNA glycosylase
KeywordsHYDROLASE/DNA / DNA glycosylase / DNA repair / sequence context / lesion recognition / disulfide crosslinking / HYDROLASE-DNA complex
Function / homology
Function and homology information


DNA-formamidopyrimidine glycosylase / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / damaged DNA binding / zinc ion binding
Similarity search - Function
Formamidopyrimidine-DNA glycosylase / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain / N-terminal domain of MutM-like DNA repair proteins ...Formamidopyrimidine-DNA glycosylase / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain / N-terminal domain of MutM-like DNA repair proteins / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / DNA glycosylase/AP lyase, H2TH DNA-binding / Helicase, Ruva Protein; domain 3 - #50 / Helicase, Ruva Protein; domain 3 / Ribosomal protein S13-like, H2TH / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Formamidopyrimidine-DNA glycosylase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSung, R.J. / Zhang, M. / Qi, Y. / Verdine, G.L.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Sequence-dependent structural variation in DNA undergoing intrahelical inspection by the DNA glycosylase MutM.
Authors: Sung, R.J. / Zhang, M. / Qi, Y. / Verdine, G.L.
History
DepositionOct 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Sep 25, 2013Group: Derived calculations

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Formamidopyrimidine-DNA glycosylase
B: DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*AP*GP*GP*AP*CP*GP*C)-3')
C: DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*TP*(8OG)P*GP*TP*(CX2)P*TP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5194
Polymers40,4543
Non-polymers651
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-11 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.188, 93.541, 104.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Formamidopyrimidine-DNA glycosylase


Mass: 30580.330 Da / Num. of mol.: 1 / Mutation: E3Q, Q166C,V222P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli)
References: UniProt: P84131, DNA-formamidopyrimidine glycosylase
#2: DNA chain DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*AP*GP*GP*AP*CP*GP*C)-3')


Mass: 4957.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA
#3: DNA chain DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*TP*(8OG)P*GP*TP*(CX2)P*TP*AP*CP*C)-3')


Mass: 4916.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8K, sodium cacodylate, glycerol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→32.685 Å / Num. obs: 25999
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 3.1

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→32.685 Å / SU ML: 0.26 / σ(F): 0.21 / Phase error: 20.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2235 1219 4.82 %
Rwork0.1883 --
obs0.19 25296 94.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.943 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.3747 Å2-0 Å2-0 Å2
2---3.8965 Å20 Å2
3----1.4782 Å2
Refinement stepCycle: LAST / Resolution: 2.1→32.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1990 357 1 144 2492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052451
X-RAY DIFFRACTIONf_angle_d0.9533383
X-RAY DIFFRACTIONf_dihedral_angle_d17.219959
X-RAY DIFFRACTIONf_chiral_restr0.059374
X-RAY DIFFRACTIONf_plane_restr0.004378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.18410.25191410.20162411X-RAY DIFFRACTION88
2.1841-2.28340.21591130.18782475X-RAY DIFFRACTION89
2.2834-2.40380.25511210.17762574X-RAY DIFFRACTION93
2.4038-2.55440.2491240.18922604X-RAY DIFFRACTION93
2.5544-2.75150.22261520.18532664X-RAY DIFFRACTION96
2.7515-3.02820.22651330.19182739X-RAY DIFFRACTION97
3.0282-3.4660.22961430.19932795X-RAY DIFFRACTION99
3.466-4.36510.18891440.17052831X-RAY DIFFRACTION100
4.3651-32.68850.21211480.18222984X-RAY DIFFRACTION99
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)
1-0.22380.12590.05631.19821.12941.103-0.0134-0.06250.01940.0062-0.14650.1095-0.0176-0.0860.14170.03820.0124-0.00540.1445-0.05270.079113.7583-4.106517.2455
24.626-4.626-1.96186.49621.41710.9541-0.36350.0834-0.53750.7446-0.02990.83170.08840.00370.37040.3278-0.14230.06470.3233-0.04550.34614.2966-11.748726.1734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B or chain C

+
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