[English] 日本語
Yorodumi- PDB-5dqn: Polyethylene 600-bound form of P450 CYP125A3 mutant from Myobacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dqn | ||||||
---|---|---|---|---|---|---|---|
Title | Polyethylene 600-bound form of P450 CYP125A3 mutant from Myobacterium Smegmatis - W83Y | ||||||
Components | Cytochrome P450 CYP125 | ||||||
Keywords | OXIDOREDUCTASE / CHOLESTEROL METABOLISM | ||||||
Function / homology | Function and homology information cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming] / cholest-4-en-3-one 26-monooxygenase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.262 Å | ||||||
Authors | Ortiz de Montellano, P.J. / Frank, D.J. / Waddling, C.A. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Biochemistry / Year: 2015 Title: Cytochrome P450 125A4, the Third Cholesterol C-26 Hydroxylase from Mycobacterium smegmatis. Authors: Frank, D.J. / Waddling, C.A. / La, M. / Ortiz de Montellano, P.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5dqn.cif.gz | 184.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5dqn.ent.gz | 144.5 KB | Display | PDB format |
PDBx/mmJSON format | 5dqn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dqn_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5dqn_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5dqn_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 5dqn_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/5dqn ftp://data.pdbj.org/pub/pdb/validation_reports/dq/5dqn | HTTPS FTP |
-Related structure data
Related structure data | 4apyS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 46996.734 Da / Num. of mol.: 1 / Mutation: W83Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: cyp125, MSMEI_5834 / Plasmid: PCW / Production host: Escherichia coli (E. coli) / Strain (production host): DH5(Alpha) References: UniProt: I7G9K1, UniProt: A0R4Y3*PLUS, EC: 1.14.13.151 |
---|
-Non-polymers , 5 types, 91 molecules
#2: Chemical | ChemComp-HEM / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | ChemComp-CIT / | #5: Chemical | ChemComp-1PE / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.74 Å3/Da / Density % sol: 67.13 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: Well contents (JCSG Core-III screen, G4): 0.1M Phosphate-Citrate buffer, pH 4.2 PEG 600, 40% v/v Drop Contents: 90% Well contents (see above) 10% Silver Bullets screen, B18: - 0.33% w/v 2,6- ...Details: Well contents (JCSG Core-III screen, G4): 0.1M Phosphate-Citrate buffer, pH 4.2 PEG 600, 40% v/v Drop Contents: 90% Well contents (see above) 10% Silver Bullets screen, B18: - 0.33% w/v 2,6-Naphthalenedisulfonic acid disodium salt - 0.33% w/v 2-Aminobenzenedisulfonic acid - 0.33% w/v m-Benzenedisulfonic acid disodium salt 0.02M HEPES sodium, pH 6.8 |
-Data collection
Diffraction | Mean temperature: 98 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11585 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11585 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→80.322 Å / Num. obs: 32185 / % possible obs: 99.67 % / Redundancy: 2 % / Biso Wilson estimate: 51.5 Å2 / Rmerge(I) obs: 0.04274 / Net I/σ(I): 19.37 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4APY Resolution: 2.262→80.247 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0.95 / Phase error: 23.14 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.262→80.247 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|