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Open data
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Basic information
Entry | Database: PDB / ID: 1uyu | ||||||
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Title | Xenon COMPLEX OF wildtype P450CAM FROM PSEUDOMONAS PUTIDA | ||||||
![]() | CYTOCHROME P450-CAM | ||||||
![]() | OXIDOREDUCTASE / MONO-OXYGENASE / HEME / ELECTRON TRANSPORT | ||||||
Function / homology | ![]() camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wade, R.C. / Winn, P.J. / Schlichting, I. / Sudarko, X. | ||||||
![]() | ![]() Title: A Survey of Active Site Access Channels in Cytochromes P450 Authors: Wade, R.C. / Winn, P.J. / Schlichting, I. #1: Journal: Annu.Rev.Biochem. / Year: 2004 Title: Structural Aspects of Ligand Binding to and Electron Transfer in Bacterial and Fungal P450S Authors: Pylypenko, O. / Schlichting, I. #2: ![]() Title: High-Resolution Crystal Structure of Cytochrome P450Cam Authors: Poulos, T.L. / Finzel, B.C. / Howard, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 186.4 KB | Display | ![]() |
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PDB format | ![]() | 147.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 36.1 KB | Display | |
Data in CIF | ![]() | 52.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dz8S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46587.895 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: HEME ATTACHED VIA CYS357, XENON BOUND IN CAVITIES / Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 467 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/CAM.gif)
![](data/chem/img/K.gif)
![](data/chem/img/XE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CAM.gif)
![](data/chem/img/K.gif)
![](data/chem/img/XE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-XE / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.55 % Description: A CRYOCOOLED, LOOP MOUNTED P450 CRYSTAL CONTAINING CAMPHOR AND HEME-BOUND CYANIDE (NO CYANIDE IN THE CRYOPROTECTANT CONTAINING 20% GLYCEROL) WAS WARMED UP QUICKLY AND MOUNTED IN A HOME- ...Description: A CRYOCOOLED, LOOP MOUNTED P450 CRYSTAL CONTAINING CAMPHOR AND HEME-BOUND CYANIDE (NO CYANIDE IN THE CRYOPROTECTANT CONTAINING 20% GLYCEROL) WAS WARMED UP QUICKLY AND MOUNTED IN A HOME-BUILT PRESSURE CELL. THE CRYSTAL WAS EXPOSED FOR 3 MIN. TO 7 BAR XENON AT 2 DEG. C SUBSEQUENTLY, THE CRYSTAL WAS FLASH COOLED IN LIQUID NITROGEN. |
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Crystal grow | Temperature: 275 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: CRYSTALS WERE GROWN USING THE SITTING DROP GEOMETRY AT 2 DEG. C. 5 UL OF 30 MG/ML P450 IN 50 MM TRIS HCL, 250 MM KCL, 0.5 MM CAMPHOR WERE MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION ...Details: CRYSTALS WERE GROWN USING THE SITTING DROP GEOMETRY AT 2 DEG. C. 5 UL OF 30 MG/ML P450 IN 50 MM TRIS HCL, 250 MM KCL, 0.5 MM CAMPHOR WERE MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION (27-30% PEG 4000, 100 MM DTE, SAME BUFFER AS PROTEIN)., pH 7.40 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: MONO / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2→19 Å / Num. obs: 53282 / % possible obs: 99.7 % / Redundancy: 3.82 % / Biso Wilson estimate: 32.91 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 4.2 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DZ8 Resolution: 2→19.84 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.249 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. N-TERMINUS IS DISORDERED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.84 Å
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Refine LS restraints |
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