[English] 日本語
Yorodumi- PDB-2ore: Binary Structure of Escherichia coli DNA Adenine Methyltransferas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ore | ||||||
---|---|---|---|---|---|---|---|
Title | Binary Structure of Escherichia coli DNA Adenine Methyltransferase and S-adenosylhomocysteine | ||||||
Components | DNA adenine methylase | ||||||
Keywords | TRANSFERASE / DAM METHYLATION / GATC RECOGNITION / S-ADENOSYLHOMOCYSTEINE CONFORMATION / BACTERIAL VIRULENCE FACTOR | ||||||
Function / homology | Function and homology information bacterial-type DNA replication initiation / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / S-adenosyl-L-methionine binding / DNA restriction-modification system / mismatch repair / response to UV / DNA-templated DNA replication / sequence-specific DNA binding / methylation Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å | ||||||
Authors | Horton, J.R. / Cheng, X. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Two Alternative Conformations of S-Adenosyl-L-homocysteine Bound to Escherichia coli DNA Adenine Methyltransferase and the Implication of Conformational Changes in Regulating the Catalytic Cycle. Authors: Liebert, K. / Horton, J.R. / Chahar, S. / Orwick, M. / Cheng, X. / Jeltsch, A. #1: Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ore.cif.gz | 161.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ore.ent.gz | 126.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ore.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ore_validation.pdf.gz | 672.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2ore_full_validation.pdf.gz | 693.3 KB | Display | |
Data in XML | 2ore_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 2ore_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/2ore ftp://data.pdbj.org/pub/pdb/validation_reports/or/2ore | HTTPS FTP |
-Related structure data
Related structure data | 2g1pS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34314.961 Da / Num. of mol.: 3 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) #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.61 Å3/Da / Density % sol: 65.9 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 1.5 M lithium sulfate,50mM magnesium sulfate, 100mM HEPES pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 173 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97923 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 18, 2005 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→34.67 Å / Num. all: 28266 / Num. obs: 28125 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.111 |
Reflection shell | Resolution: 2.99→3.1 Å / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2G1P Resolution: 2.99→34.67 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.9 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.99→34.67 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|