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- PDB-2z3u: Crystal Structure of Chromopyrrolic Acid Bound Cytochrome P450 St... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2z3u | ||||||
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Title | Crystal Structure of Chromopyrrolic Acid Bound Cytochrome P450 StaP (CYP245A1) | ||||||
![]() | Cytochrome P450 | ||||||
![]() | OXIDOREDUCTASE / cytochrome P450 / monoxygenase / oxydoreductase / heme-enzyme / chromopyrrolic acid | ||||||
Function / homology | ![]() cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Makino, M. / Sugimoto, H. / Shiro, Y. / Asamizu, S. / Onaka, H. / Nagano, S. | ||||||
![]() | ![]() Title: Crystal structures and catalytic mechanism of cytochrome P450 StaP that produces the indolocarbazole skeleton Authors: Makino, M. / Sugimoto, H. / Shiro, Y. / Asamizu, S. / Onaka, H. / Nagano, S. #1: ![]() Title: Theoretical and experimental studies of the conversion of chromopyrrolic acid to an antitumor derivative by cytochrome P450 StaP: the catalytic role of water molecules Authors: Wang, Y. / Chen, H. / Makino, M. / Shiro, Y. / Nagano, S. / Asamizu, S. / Onaka, H. / Shaik, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.2 KB | Display | ![]() |
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PDB format | ![]() | 77.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 29.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2z3tSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47262.262 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.8 Details: 2% PEG 4000, 50mM Bis-Tris pH 6.8, 100mM magnesium chloride, 10mM manganese chloride, 5mM chromopyrrolic acid, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 15, 2006 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 16573 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 20.2 Å2 / Rsym value: 0.074 / Net I/σ(I): 22.46 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 6.06 / Num. unique all: 1626 / Rsym value: 0.324 / % possible all: 97.7 |
-Phasing
Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Z3T Resolution: 2.4→19.96 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1570890.875 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.309 Å2 / ksol: 0.356 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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