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Yorodumi- PDB-2uvn: Crystal structure of econazole-bound CYP130 from Mycobacterium tu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uvn | ||||||
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Title | Crystal structure of econazole-bound CYP130 from Mycobacterium tuberculosis | ||||||
Components | CYTOCHROME P450 130 | ||||||
Keywords | OXIDOREDUCTASE / IRON / HEME / MONOOXYGENASE / METAL-BINDING | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / cell wall / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / monooxygenase activity / peptidoglycan-based cell wall / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Podust, L.M. / Ortiz de Montellano, P.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Mycobacterium Tuberculosis Cyp130: Crystal Structure, Biophysical Characterization, and Interactions with Antifungal Azole Drugs Authors: Ouellet, H. / Podust, L.M. / Ortiz de Montellano, P.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uvn.cif.gz | 170.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uvn.ent.gz | 134.4 KB | Display | PDB format |
PDBx/mmJSON format | 2uvn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2uvn_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 2uvn_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 2uvn_validation.xml.gz | 34.6 KB | Display | |
Data in CIF | 2uvn_validation.cif.gz | 45.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/2uvn ftp://data.pdbj.org/pub/pdb/validation_reports/uv/2uvn | HTTPS FTP |
-Related structure data
Related structure data | 2uuqSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.79352, -0.52541, -0.30702), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45836.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PCWORI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q11062, UniProt: P9WPN5*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen |
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-Non-polymers , 5 types, 99 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-F / #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | 6XHIS-TAG AT THE N-TERMINUS SER 406 AND R 407 ARE INTRODUCED AT THE C-TERMINUS AS A RESULT OF ...6XHIS-TAG AT THE N-TERMINUS SER 406 AND R 407 ARE INTRODUCED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.65 Å3/Da / Density % sol: 78 % / Description: NONE |
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Crystal grow | pH: 6.25 Details: 1.4 M AMMONIUM SULFATE, 0.1 M MES, PH 6.25, 40 MM NAF |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 26, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11588 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 45935 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 29.9 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 4.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2UUQ Resolution: 3→49.67 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 40310.97 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF Details: BULK SOLVENT MODEL USED. DISORDERED REGIONS WERE OMITTED FROM THE CRYSTAL STRUCTURE
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.2059 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→49.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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