[English] 日本語
Yorodumi
- PDB-4zyd: Crystal structure of Sulfolobus solfataricus O6-methylguanine met... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zyd
TitleCrystal structure of Sulfolobus solfataricus O6-methylguanine methyltransferase in complex with modified DNA
Components
  • DNA (5'-D(*GP*CP*CP*AP*TP*GP*(6OG)P*CP*TP*AP*GP*TP*A)-3')
  • DNA (5'-D(*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3')
  • Methylated-DNA--protein-cysteine methyltransferase
KeywordsTRANSFERASE / Extremophiles / DNA repair / Alkylated DNA-protein alkyltransferase / protein-DNA complex / cell cycle
Function / homology
Function and homology information


methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / DNA alkylation repair / methylation / cytoplasm
Similarity search - Function
Methylated-DNA--protein-cysteine methyltransferase / Methylated DNA-protein cysteine methyltransferase domain / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / Methylated-DNA--protein-cysteine methyltransferase active site. / Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding / Methylated DNA-protein cysteine methyltransferase, DNA binding domain / 6-O-methylguanine DNA methyltransferase, DNA binding domain ...Methylated-DNA--protein-cysteine methyltransferase / Methylated DNA-protein cysteine methyltransferase domain / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / Methylated-DNA--protein-cysteine methyltransferase active site. / Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding / Methylated DNA-protein cysteine methyltransferase, DNA binding domain / 6-O-methylguanine DNA methyltransferase, DNA binding domain / Double Stranded RNA Binding Domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Methylated-DNA--protein-cysteine methyltransferase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.682 Å
AuthorsMiggiano, R. / Rossi, F. / Rizzi, M.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structure-function relationships governing activity and stability of a DNA alkylation damage repair thermostable protein.
Authors: Perugino, G. / Miggiano, R. / Serpe, M. / Vettone, A. / Valenti, A. / Lahiri, S. / Rossi, F. / Rossi, M. / Rizzi, M. / Ciaramella, M.
History
DepositionMay 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methylated-DNA--protein-cysteine methyltransferase
B: DNA (5'-D(*GP*CP*CP*AP*TP*GP*(6OG)P*CP*TP*AP*GP*TP*A)-3')
C: DNA (5'-D(*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)24,9853
Polymers24,9853
Non-polymers00
Water1086
1
A: Methylated-DNA--protein-cysteine methyltransferase

B: DNA (5'-D(*GP*CP*CP*AP*TP*GP*(6OG)P*CP*TP*AP*GP*TP*A)-3')
C: DNA (5'-D(*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)24,9853
Polymers24,9853
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
Buried area3310 Å2
ΔGint-10 kcal/mol
Surface area11280 Å2
MethodPISA
2
B: DNA (5'-D(*GP*CP*CP*AP*TP*GP*(6OG)P*CP*TP*AP*GP*TP*A)-3')
C: DNA (5'-D(*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3')

A: Methylated-DNA--protein-cysteine methyltransferase


Theoretical massNumber of molelcules
Total (without water)24,9853
Polymers24,9853
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_456x-1/2,-y+1/2,-z+11
Buried area3310 Å2
ΔGint-10 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.764, 65.879, 97.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Methylated-DNA--protein-cysteine methyltransferase / 6-O-methylguanine-DNA methyltransferase / MGMT / O-6-methylguanine-DNA-alkyltransferase


Mass: 17027.996 Da / Num. of mol.: 1 / Mutation: C119A
Source method: isolated from a genetically manipulated source
Details: Methionine at position 1 and glutamic acid at position 151 were not detected in electron density map. Therefore, they were excluded from the coordinate file.
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: ogt, SSO2487 / Plasmid: pQE31 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q97VW7, methylated-DNA-[protein]-cysteine S-methyltransferase
#2: DNA chain DNA (5'-D(*GP*CP*CP*AP*TP*GP*(6OG)P*CP*TP*AP*GP*TP*A)-3')


Mass: 4005.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3')


Mass: 3951.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG 3350, Na/K tartrate 0.2 M

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9724 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.67→41.76 Å / Num. obs: 7993 / % possible obs: 99.7 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 10.6
Reflection shellHighest resolution: 2.67 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.7 / % possible all: 90.9

-
Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WRJ

1wrj


Resolution: 2.682→39.195 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2712 370 4.67 %
Rwork0.2134 --
obs0.2164 7916 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.682→39.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 528 0 6 1713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011798
X-RAY DIFFRACTIONf_angle_d1.3242534
X-RAY DIFFRACTIONf_dihedral_angle_d24.403708
X-RAY DIFFRACTIONf_chiral_restr0.054281
X-RAY DIFFRACTIONf_plane_restr0.006230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6822-3.07020.40111230.29472421X-RAY DIFFRACTION98
3.0702-3.86760.29261120.24322506X-RAY DIFFRACTION99
3.8676-39.19890.24111350.1862619X-RAY DIFFRACTION100

+
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