[English] 日本語
Yorodumi- PDB-2zi8: Crystal structure of the HsaC extradiol dioxygenase from M. tuber... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zi8 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the HsaC extradiol dioxygenase from M. tuberculosis in complex with 3,4-dihydroxy-9,10-seconandrost-1,3,5(10)-triene-9,17-dione (DHSA) | ||||||
Components | PROBABLE BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE BPHC | ||||||
Keywords | OXIDOREDUCTASE / DHSA / HsaC / extradiol dioxygenase / Mycobacterium tuberculosis / Aromatic hydrocarbons catabolism / Iron | ||||||
Function / homology | Function and homology information 3,4-dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione 4,5-dioxygenase / 3,4-dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione 4,5-dioxygenase activity / cholesterol catabolic process / response to cholesterol / : / lipid catabolic process / cholesterol metabolic process / ferrous iron binding / iron ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | D'Angelo, I. / Yam, K.C. / Eltis, L.D. / Strynadka, N. | ||||||
Citation | Journal: Plos Pathog. / Year: 2009 Title: Studies of a ring-cleaving dioxygenase illuminate the role of cholesterol metabolism in the pathogenesis of Mycobacterium tuberculosis. Authors: Yam, K.C. / D'Angelo, I. / Kalscheuer, R. / Zhu, H. / Wang, J.X. / Snieckus, V. / Ly, L.H. / Converse, P.J. / Jacobs, W.R. / Strynadka, N. / Eltis, L.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2zi8.cif.gz | 142.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2zi8.ent.gz | 111.3 KB | Display | PDB format |
PDBx/mmJSON format | 2zi8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/2zi8 ftp://data.pdbj.org/pub/pdb/validation_reports/zi/2zi8 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2zyqC 1hanS 2zf1 S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33628.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Plasmid: pT7HC1 / Production host: Escherichia coli (E. coli) / Strain (production host): GJ1158 References: UniProt: P96850, UniProt: P9WNW7*PLUS, biphenyl-2,3-diol 1,2-dioxygenase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.75 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 12-15% PEG 3350, 0.2M ammonium tartrate, 25% ethylene glycol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2007 / Details: MC |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 56012 / Num. obs: 55996 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 26 |
Reflection shell | Resolution: 2.2→2.32 Å / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 6.1 / Num. unique all: 6156 / Rsym value: 0.389 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HAN Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.884 / SU B: 6.703 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.224 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.477 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
|