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Open data
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Basic information
Entry | Database: PDB / ID: 1dz9 | ||||||
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Title | Putative oxo complex of P450cam from Pseudomonas putida | ||||||
![]() | CYTOCHROME P450-CAM | ||||||
![]() | OXIDOREDUCTASE / MONO-OXYGENASE / HEME / REACTION INTERMEDIATE | ||||||
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 | ![]() ![]() | ||||||
![]() | Schlichting, I. / Berendzen, J. / Chu, K. / Stock, A.M. / Maves, S.A. / Benson, D.E. / Sweet, R.M. / Ringe, D. / Petsko, G.A. / Sligar, S.G. | ||||||
![]() | ![]() Title: The Catalytic Pathway of Cytochrome P450Cam at Atomic Resolution Authors: Schlichting, I. / Berendzen, J. / Chu, K. / Stock, A.M. / Maves, S.A. / Benson, D.E. / Sweet, R.M. / Ringe, D. / Petsko, G.A. / Sligar, S.G. #1: ![]() Title: Understanding the Role of the Essential Asp251 in Cytochrome P450Cam Using Site-Directed Mcrystallography, and Kinetic Solvent Isotope Effectutagenesis, N Authors: Vidakovic, M. / Sligar, S.G. / Li, H. / Poulos, T.L. #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 | ![]() | 194.1 KB | Display | ![]() |
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PDB format | ![]() | 152 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 | ![]() | 42.1 KB | Display | |
Data in CIF | ![]() | 61.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9735, 0.016, 0.228), Vector: Details | BIOLOGICAL_UNIT: MONOMER | |
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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: OXYGEN BOUND TO HEME IRON. HEME ATTACHED VIA CYS357 Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 718 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/O.gif)
![](data/chem/img/CAM.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/O.gif)
![](data/chem/img/CAM.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-O / | #4: Chemical | #5: Chemical | ChemComp-TRS / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | N-TERMINUS IS DISORDERED THE ELECTRON DENSITY CORRESPONDING TO THE SIXTH LIGAND AT THE HEME IN ...N-TERMINUS IS DISORDERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.3 % Description: THE CRYSTAL WAS REDUCED BY SOAKING IN NITROGENATED RESERVOIR SOLUTION CONTAINING 50 MM DITHIONATE, 40 MM NAOH UNTIL A CLEAR COLOUR CHANGE OCCURED. THE OXYGEN COMPLEX WAS PREPARED BY ...Description: THE CRYSTAL WAS REDUCED BY SOAKING IN NITROGENATED RESERVOIR SOLUTION CONTAINING 50 MM DITHIONATE, 40 MM NAOH UNTIL A CLEAR COLOUR CHANGE OCCURED. THE OXYGEN COMPLEX WAS PREPARED BY EXPOSING THE CRYSTAL FOR 3 MIN. TO 120 BAR OXYGEN AT 2 DEG. C USING A PRESSURE CELL. 20% GLYCEROL WAS USED AS CRYOPROTECTANT, THE CRYSTALS WERE FREEZE QUENCHED IN LIQUID NITROGEN. AFTER COLLECTION OF A DATASET USING 0.91 A WAVELENGTH X-RAYS, THE CRYSTAL WAS ILLUMINATED FOR 3 HOURS WITH 1.5 A WAVELENGTH X-RAYS AND A SECOND DATASET WAS COLLECTED WITH 0.91 A X-RAYS. | |||||||||||||||||||||||||||||||||||||||||||||||||
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting dropDetails: drop consists of equal volume of protein and reservoir solutions pH: 7.4 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 96 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: BRANDEIS / Detector: CCD / Date: Oct 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→39 Å / Num. obs: 66465 / % possible obs: 92.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.1 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.333 / % possible all: 59.2 |
Reflection | *PLUS Rmerge(I) obs: 0.1 |
Reflection shell | *PLUS % possible obs: 59.2 % / Rmerge(I) obs: 0.333 |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 1.9→19 Å / SU B: 4.82237 / SU ML: 0.13688 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17864 / ESU R Free: 0.17393
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Refinement step | Cycle: LAST / Resolution: 1.9→19 Å
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Refine LS restraints |
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