[English] 日本語
Yorodumi- PDB-4hgf: Crystal structure of P450 BM3 5F5K heme domain variant complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hgf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of P450 BM3 5F5K heme domain variant complexed with styrene | ||||||
Components | Bifunctional P-450/NADPH-P450 reductase | ||||||
Keywords | OXIDOREDUCTASE / P450 BM3 / hemoprotein / styrene epoxidation / inverted enantioselectivity / Heme binding | ||||||
Function / homology | Function and homology information NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / metabolic process / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding ...NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / metabolic process / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Bacillus megaterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Shehzad, A. / Panneerselvam, S. / Bocola, M. / Mueller-Dieckmann, J. / Wilmanns, M. / Schwaneberg, U. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2013 Title: P450 BM3 crystal structures reveal the role of the charged surface residue Lys/Arg184 in inversion of enantioselective styrene epoxidation. Authors: Shehzad, A. / Panneerselvam, S. / Linow, M. / Bocola, M. / Roccatano, D. / Mueller-Dieckmann, J. / Wilmanns, M. / Schwaneberg, U. #1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2006 Title: A screening system for the directed evolution of epoxygenases: importance of position 184 in P450 BM3 for stereoselective styrene epoxidation. Authors: Tee, K.L. / Schwaneberg, U. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4hgf.cif.gz | 211.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4hgf.ent.gz | 167.3 KB | Display | PDB format |
PDBx/mmJSON format | 4hgf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/4hgf ftp://data.pdbj.org/pub/pdb/validation_reports/hg/4hgf | HTTPS FTP |
---|
-Related structure data
Related structure data | 4hggC 4hghC 4hgiC 4hgjC 2j4sS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 52121.441 Da / Num. of mol.: 2 / Fragment: Heme-binding domain / Mutation: F87A, A184K, T235A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: cyp102, cyp102A1 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.84 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 300 mM magnesium formate, 100 mM tris(hydroxymethyl)aminomethane (pH 8.5), 200 mM sodium malonate/110 mM potassium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 27, 2010 / Details: mirrors |
Radiation | Monochromator: Si 111 HORIZONTALLY FOCUSSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19.51 Å / Num. all: 119333 / Num. obs: 117395 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 5 / Redundancy: 3.3 % / Biso Wilson estimate: 27.49 Å2 / Net I/σ(I): 10.99 |
Reflection shell | Resolution: 1.7→1.781 Å / Num. unique all: 15432 / % possible all: 99.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J4S Resolution: 1.7→19.51 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.141 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→19.51 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
|