[English] 日本語
Yorodumi- PDB-1rf9: Crystal structure of cytochrome P450-cam with a fluorescent probe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rf9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of cytochrome P450-cam with a fluorescent probe D-4-AD (Adamantane-1-carboxylic acid-5-dimethylamino-naphthalene-1-sulfonylamino-butyl-amide) | ||||||
Components | Cytochrome P450-cam | ||||||
Keywords | OXIDOREDUCTASE / MONOOXYGENASE / CONFORMATIONAL STATES / SUBSTRATE-LINKED SENSITIZERS / SUBSTRATE-BINDING / DANSYL / ADAMANTANE / ADAMANTANE-1-CARBOXYLIC ACID [4-(5-DIMETHYLAMINO-NAPHTHALENE-1-SULFONYLAMINO)-BUTYL]-AMIDE / CHANNEL | ||||||
Function / homology | Function and homology information 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 | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Hays, A.-M.A. / Dunn, A.R. / Gray, H.B. / Stout, C.D. / Goodin, D.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Conformational States of Cytochrome P450cam Revealed by Trapping of synthetic Molecular Wires Authors: Hays, A.-M.A. / Dunn, A.R. / Chiu, R. / Gray, H.B. / Stout, C.D. / Goodin, D.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1rf9.cif.gz | 104 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1rf9.ent.gz | 77.1 KB | Display | PDB format |
PDBx/mmJSON format | 1rf9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rf9_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1rf9_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1rf9_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 1rf9_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/1rf9 ftp://data.pdbj.org/pub/pdb/validation_reports/rf/1rf9 | HTTPS FTP |
-Related structure data
Related structure data | 1re9C 2cppS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 46961.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: CAMC, CYP101 / Plasmid: PUS200 / Production host: Escherichia coli (E. coli) / Strain (production host): TBY / References: UniProt: P00183, camphor 5-monooxygenase |
---|---|
#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-DBR / |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.27 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: CITRATE, PEG, KCL, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 105 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 27, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 38960 / Num. obs: 32283 / % possible obs: 90.7 % / Observed criterion σ(I): 2 / Redundancy: 3.15 % / Biso Wilson estimate: 19.83 Å2 / Rsym value: 0.063 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.34 / % possible all: 88.6 |
-Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CPP Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å / Luzzati sigma a obs: 0.21 Å | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
| ||||||||||||||||
Refine LS restraints |
|