[English] 日本語
Yorodumi
- PDB-2g1p: Structure of E. coli DNA adenine methyltransferase (DAM) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2g1p
TitleStructure of E. coli DNA adenine methyltransferase (DAM)
Components
  • 5'-D(*TP*CP*TP*AP*GP*AP*TP*CP*TP*AP*GP*A)-3'
  • DNA adenine methylase
KeywordsTRANSFERASE/DNA / Dam methylation / GATC recognition / Base flipping / Bacterial virulence factor / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


bacterial-type DNA replication initiation / macromolecule modification / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / S-adenosyl-L-methionine binding / mismatch repair / response to UV / DNA-templated DNA replication / methylation / sequence-specific DNA binding
Similarity search - Function
Adenine-specific Methyltransferase; domain 2 / Adenine-specific Methyltransferase, Domain 2 / Adenine modification methylase, M.EcoRV-type / D12 class N6 adenine-specific DNA methyltransferase / Adenine-specific methyltransferase, domain 2 / D12 class N6 adenine-specific DNA methyltransferase / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...Adenine-specific Methyltransferase; domain 2 / Adenine-specific Methyltransferase, Domain 2 / Adenine modification methylase, M.EcoRV-type / D12 class N6 adenine-specific DNA methyltransferase / Adenine-specific methyltransferase, domain 2 / D12 class N6 adenine-specific DNA methyltransferase / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / DNA adenine methylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsHorton, J.R. / Liebert, K. / Bekes, M. / Jeltsch, A. / Cheng, X.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase.
Authors: Horton, J.R. / Liebert, K. / Bekes, M. / Jeltsch, A. / Cheng, X.
History
DepositionFeb 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE AUTHOR STATES THAT RESIDUES 175 WERE MODELED AS SER INSTEAD OF ALA FOR BOTH MOLECULES ...SEQUENCE AUTHOR STATES THAT RESIDUES 175 WERE MODELED AS SER INSTEAD OF ALA FOR BOTH MOLECULES (CHAINS A AND B) BECAUSE OF EXTRA DENSITY.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: 5'-D(*TP*CP*TP*AP*GP*AP*TP*CP*TP*AP*GP*A)-3'
G: 5'-D(*TP*CP*TP*AP*GP*AP*TP*CP*TP*AP*GP*A)-3'
A: DNA adenine methylase
B: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5037
Polymers71,6424
Non-polymers8613
Water5,657314
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.2, 71.3, 97.8
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: DNA chain 5'-D(*TP*CP*TP*AP*GP*AP*TP*CP*TP*AP*GP*A)-3'


Mass: 3661.416 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein DNA adenine methylase / Deoxyadenosyl-methyltransferase / DNA adenine methyltransferase / M.EcoDam


Mass: 32159.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dam / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: P0AEE8, site-specific DNA-methyltransferase (adenine-specific)
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM KCl, 10 mM MgSO4, 5-15% PEG400, 100 mM MES or HEPES (pH 6.6-7.4), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1KCl11
2MgSO411
3PEG40011
4MES11
5HEPES11
6H2O11
7KCl12
8MgSO412
9PEG40012
10H2O12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97179 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97179 Å / Relative weight: 1
ReflectionResolution: 1.89→33.6 Å / Num. all: 51126 / Num. obs: 51126 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 9.1
Reflection shellResolution: 1.89→1.92 Å / Rmerge(I) obs: 0.575 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
GLRFphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Modified PDB entry 2DPM

2dpm


Resolution: 1.89→33.6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 303712.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2437 5 %RANDOM
Rwork0.188 ---
all0.188 51126 --
obs0.188 51126 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.2817 Å2 / ksol: 0.391587 e/Å3
Displacement parametersBiso mean: 29.8 Å2
Baniso -1Baniso -2Baniso -3
1-12.07 Å20 Å20 Å2
2---9 Å20 Å2
3----3.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-35 Å
Luzzati sigma a0.21 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.89→33.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4001 486 58 314 4859
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_mcbond_it1.011.5
X-RAY DIFFRACTIONc_mcangle_it1.582
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.822.5
LS refinement shellResolution: 1.89→1.92 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 116 5.2 %
Rwork0.278 2123 -
obs-2123 85.5 %

+
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://pdbjlvh1.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