[English] 日本語
Yorodumi- PDB-7xzk: Crystal Structure of P450BM3 with N-(3-cyclohexylpropanoyl)-L-pip... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xzk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of P450BM3 with N-(3-cyclohexylpropanoyl)-L-pipecolyl-L-phenylalanine | ||||||
Components | Bifunctional cytochrome P450/NADPH--P450 reductase | ||||||
Keywords | OXIDOREDUCTASE / Monooxygenase | ||||||
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 / FMN binding / iron ion binding / heme binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Priestia megaterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | ||||||
Authors | Shoji, O. / Yonemura, K. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: To Be Published Title: Crystal Structure of P450BM3 with N-(3-cyclohexylpropanoyl)-L-pipecolyl-L-phenylalanine Authors: Ariyasu, S. / Yonemura, K. / Kasai, C. / Aiba, Y. / Onoda, H. / Shisaka, Y. / Sugimoto, H. / Tosha, T. / Kubo, M. / Kamachi, T. / Yoshizawa, K. / Shoji, O. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7xzk.cif.gz | 211.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7xzk.ent.gz | 165.6 KB | Display | PDB format |
PDBx/mmJSON format | 7xzk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/7xzk ftp://data.pdbj.org/pub/pdb/validation_reports/xz/7xzk | HTTPS FTP |
---|
-Related structure data
Related structure data | 6jlvS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 52300.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Priestia megaterium (bacteria) / Gene: cyp102A1 / Production host: Escherichia coli (E. coli) References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.25 % |
---|---|
Crystal grow | Temperature: 293 K / Method: batch mode / pH: 7.9 Details: Tris-HCl, 0.1% (v/v) methanol, 0.1mM (3-cyclohexylpropanoyl)-L-pipecolyl-L-phenylalanine, MgCl, PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.54→47.48 Å / Num. obs: 154423 / % possible obs: 97.8 % / Redundancy: 2.68 % / Biso Wilson estimate: 25.058 Å2 / CC1/2: 0.964 / Rmerge(I) obs: 0.196 / Rrim(I) all: 0.241 / Χ2: 0.727 / Net I/σ(I): 4.32 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JLV Resolution: 1.54→47.48 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.0884 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 71.57 Å2 / Biso mean: 19.318 Å2 / Biso min: 8.97 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.54→47.48 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.54→1.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|