+Open data
-Basic information
Entry | Database: PDB / ID: 8spc | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the cytochrome P450 enzyme RufO | ||||||
Components | Cytochrome P450 | ||||||
Keywords | METAL BINDING PROTEIN / RufO / Aromatic nitration / Cytochrome 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 | Streptomyces atratus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.871 Å | ||||||
Authors | Dratch, B.D. / Davis, K.M. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2023 Title: Insights into Substrate Recognition by the Unusual Nitrating Enzyme RufO. Authors: Dratch, B.D. / McWhorter, K.L. / Blue, T.C. / Jones, S.K. / Horwitz, S.M. / Davis, K.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8spc.cif.gz | 104.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8spc.ent.gz | 69.4 KB | Display | PDB format |
PDBx/mmJSON format | 8spc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8spc_validation.pdf.gz | 801.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8spc_full_validation.pdf.gz | 804.5 KB | Display | |
Data in XML | 8spc_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 8spc_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sp/8spc ftp://data.pdbj.org/pub/pdb/validation_reports/sp/8spc | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 45550.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces atratus (bacteria) / Gene: rufO / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A224AU14 |
---|
-Non-polymers , 5 types, 223 molecules
#2: Chemical | ChemComp-HEM / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.2 % / Description: red, cube |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 0.2 M magnesium chloride, 0.1 M Bis-Tris, 23% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2022 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.871→39.34 Å / Num. obs: 35269 / % possible obs: 99.56 % / Redundancy: 12.8 % / Biso Wilson estimate: 40.17 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09647 / Rpim(I) all: 0.02792 / Rrim(I) all: 0.1005 / Net I/σ(I): 15.29 |
Reflection shell | Resolution: 1.871→1.937 Å / Redundancy: 8.4 % / Rmerge(I) obs: 1.469 / Mean I/σ(I) obs: 1.14 / Num. unique obs: 3398 / CC1/2: 0.687 / CC star: 0.903 / Rpim(I) all: 0.5285 / Rrim(I) all: 1.564 / % possible all: 96.32 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIR / Resolution: 1.871→39.34 Å / SU ML: 0.2309 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5635 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.871→39.34 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|