[English] 日本語
Yorodumi- PDB-8gm2: Crystal structure of T252E-CYP199A4 in complex with 4-methoxybenz... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gm2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of T252E-CYP199A4 in complex with 4-methoxybenzoic acid soaked with 2 mM hydrogen peroxide | ||||||
Components | Cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / cytochrome / bacterial P450 | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Rhodopseudomonas palustris HaA2 (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Lee, J.H.Z. / Bruning, J.B. / Bell, S.G. | ||||||
Funding support | Australia, 1items
| ||||||
Citation | Journal: Chemistry / Year: 2024 Title: An In Crystallo Reaction with an Engineered Cytochrome P450 Peroxygenase. Authors: Lee, J.H.Z. / Bruning, J.B. / Bell, S.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8gm2.cif.gz | 93.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8gm2.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 8gm2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/8gm2 ftp://data.pdbj.org/pub/pdb/validation_reports/gm/8gm2 | HTTPS FTP |
---|
-Related structure data
Related structure data | 8glyC 8glzC 8gm1C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 44601.410 Da / Num. of mol.: 1 / Mutation: T252E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris HaA2 (phototrophic) Gene: RPB_3613 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2IU02 |
---|---|
#2: Chemical | ChemComp-ANN / |
#3: Chemical | ChemComp-HEM / |
#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: 2.1 Å3/Da / Density % sol: 41.42 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.2 M magnesium acetate, 100 mM Bis-Tris buffer (adjusted with acetic acid to pH 5.0-5.75) and 20 - 32 % PEG 3350 PH range: 5.0 - 5.75 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→44.34 Å / Num. obs: 15455 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.058 / Rrim(I) all: 0.148 / Χ2: 0.95 / Net I/σ(I): 11.9 / Num. measured all: 99887 |
Reflection shell | Resolution: 2.33→2.41 Å / % possible obs: 99.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.814 / Num. measured all: 9512 / Num. unique obs: 1489 / CC1/2: 0.893 / Rpim(I) all: 0.35 / Rrim(I) all: 0.888 / Χ2: 0.98 / Net I/σ(I) obs: 3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→44.34 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 31.17 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.33→44.34 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|