[English] 日本語
Yorodumi- PDB-4hgi: Crystal structure of P450 BM3 5F5 heme domain variant complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hgi | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of P450 BM3 5F5 heme domain variant complexed with styrene (dataset II) | ||||||
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: 1.5 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 | 4hgi.cif.gz | 333.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4hgi.ent.gz | 257.2 KB | Display | PDB format |
PDBx/mmJSON format | 4hgi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hgi_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4hgi_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4hgi_validation.xml.gz | 48 KB | Display | |
Data in CIF | 4hgi_validation.cif.gz | 71.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/4hgi ftp://data.pdbj.org/pub/pdb/validation_reports/hg/4hgi | HTTPS FTP |
-Related structure data
Related structure data | 4hgfC 4hggC 4hghC 4hgjC 2j4sS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 52063.340 Da / Num. of mol.: 2 / Fragment: Heme-binding domain / Mutation: F87A, 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 |
---|
-Non-polymers , 6 types, 927 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-PEG / | #6: Chemical | ChemComp-MES / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.52 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100-160 mM magnesium chloride, 100 mM 2-(N-morpholino)ethanesulfonic acid (pH 6.5), 10-20% PEG 3350/PEG 2000 MME, 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: Oct 15, 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: 1.5→19.99 Å / Num. all: 175984 / Num. obs: 155738 / % possible obs: 88.5 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 23.4 Å2 / Net I/σ(I): 22.73 |
Reflection shell | Resolution: 1.5→1.573 Å / Num. unique all: 19343 / % possible all: 83.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J4S Resolution: 1.5→19.99 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 20.331 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→19.99 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
|