[English] 日本語
Yorodumi- PDB-4bhb: Crystal structure of Mycobacterium tuberculosis O6-METHYLGUANINE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bhb | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Mycobacterium tuberculosis O6-METHYLGUANINE METHYLTRANSFERASE | ||||||
Components | METHYLATED-DNA--PROTEIN-CYSTEINE METHYLTRANSFERASE | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / response to nitrosative stress / DNA alkylation repair / methylation / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Miggiano, R. / Casazza, V. / Garavaglia, S. / Ciaramella, M. / Perugino, G. / Rizzii, M. / Rossi, F. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2013 Title: Biochemical and Structural Studies of the Mycobacterium Tuberculosis O6-Methylguanine Methyltransferase and Mutated Variants. Authors: Miggiano, R. / Casazza, V. / Garavaglia, S. / Ciaramella, M. / Perugino, G. / Rizzi, M. / Rossi, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4bhb.cif.gz | 46.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4bhb.ent.gz | 32.6 KB | Display | PDB format |
PDBx/mmJSON format | 4bhb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bhb_validation.pdf.gz | 439.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4bhb_full_validation.pdf.gz | 440.4 KB | Display | |
Data in XML | 4bhb_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 4bhb_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/4bhb ftp://data.pdbj.org/pub/pdb/validation_reports/bh/4bhb | HTTPS FTP |
-Related structure data
Related structure data | 4bhcC 1sfeS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17864.156 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0A696, UniProt: P9WJW5*PLUS, methylated-DNA-[protein]-cysteine S-methyltransferase | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | ILE 2 HAS BEEN REPLACED BY VAL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 52 % / Description: NONE |
---|---|
Crystal grow | pH: 7.5 / Details: pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.99 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 17690 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 31.39 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SFE Resolution: 1.8→27.896 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 33.66 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.3 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→27.896 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell |
|