+Open data
-Basic information
Entry | Database: PDB / ID: 1dz8 | ||||||
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Title | oxygen complex of p450cam from pseudomonas putida | ||||||
Components | CYTOCHROME P450-CAM | ||||||
Keywords | OXIDOREDUCTASE / MONO-OXYGENASE / HEME | ||||||
Function / homology | Function and homology information camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | PSEUDOMONAS PUTIDA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.9 Å | ||||||
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. | ||||||
Citation | Journal: Science / Year: 2000 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: Journal: Biochemistry / Year: 1998 Title: Understanding the Role of the Essential Asp251 Icytochrome P450Cam Using Site-Directed Mcrystallography, and Kinetic Solvent Isotope Effectutagenesis, N Authors: Vidakovic, M. / Sligar, S.G. / Li, H. / Poulos, T.L. #2: Journal: J.Mol.Biol. / Year: 1987 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dz8.cif.gz | 186.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dz8.ent.gz | 154 KB | Display | PDB format |
PDBx/mmJSON format | 1dz8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/1dz8 ftp://data.pdbj.org/pub/pdb/validation_reports/dz/1dz8 | HTTPS FTP |
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-Related structure data
-Links
-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 | |
-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.) PSEUDOMONAS PUTIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00183 |
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-Non-polymers , 6 types, 659 molecules
#2: Chemical | #3: Chemical | ChemComp-OXY / | #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.54 % 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. | |||||||||||||||||||||||||||||||||||||||||||||||||
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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 drop / pH: 7.4 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 88 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.91 |
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: 69362 / % possible obs: 96.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.092 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.388 / % possible all: 86.1 |
Reflection | *PLUS Num. measured all: 217362 / Rmerge(I) obs: 0.092 |
Reflection shell | *PLUS % possible obs: 85 % / Rmerge(I) obs: 0.388 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.9→19 Å / SU B: 4.36518 / SU ML: 0.1276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17566 / ESU R Free: 0.17371 Details: THE ELECTRON DENSITY CORRESPONDING TO THE SIXTH LIGAND AT THE HEME IN MOLECULE B WAS NOT MODELED.
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Refinement step | Cycle: LAST / Resolution: 1.9→19 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 15 Å / Rfactor obs: 0.203 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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