[English] 日本語
Yorodumi- PDB-2zyq: Crystal structure of the HsaC extradiol dioxygenase from M. tuber... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zyq | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the HsaC extradiol dioxygenase from M. tuberculosis | ||||||
Components | PROBABLE BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE BPHC | ||||||
Keywords | OXIDOREDUCTASE / dioxygenase / extradiol / dhsa / tb / catechol / cholesterol / steroid / 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 / : / response to cholesterol / cholesterol catabolic process / lipid catabolic process / cholesterol metabolic process / ferrous iron binding / iron ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 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 | 2zyq.cif.gz | 142.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2zyq.ent.gz | 111 KB | Display | PDB format |
PDBx/mmJSON format | 2zyq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zyq_validation.pdf.gz | 456.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2zyq_full_validation.pdf.gz | 464.4 KB | Display | |
Data in XML | 2zyq_validation.xml.gz | 31 KB | Display | |
Data in CIF | 2zyq_validation.cif.gz | 47.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/2zyq ftp://data.pdbj.org/pub/pdb/validation_reports/zy/2zyq | HTTPS FTP |
-Related structure data
Related structure data | 2zi8C 1kndS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
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 / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P96850, UniProt: P9WNW7*PLUS, biphenyl-2,3-diol 1,2-dioxygenase #2: Chemical | #3: Chemical | ChemComp-TAR / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.52 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: pH 6.80, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 / Wavelength: 1.541 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 20, 2006 |
Radiation | Monochromator: OSMIC VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 2→26 Å / Num. all: 56597 / Num. obs: 56445 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 14 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.091 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2→2.2 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.441 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KND Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.222 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.143 / 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: 19.41 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
|