+Open data
-Basic information
Entry | Database: PDB / ID: 7x2q | ||||||
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Title | Salvia miltiorrhiza CYP76AH3 | ||||||
Components | Sugiol synthase | ||||||
Keywords | OXIDOREDUCTASE / P450 protein / MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information ferruginol monooxygenase / sugiol synthase / terpenoid biosynthetic process / 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 / iron ion binding / heme binding / membrane Similarity search - Function | ||||||
Biological species | Salvia miltiorrhiza (Chinese salvia) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.68 Å | ||||||
Authors | Chang, Z. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure of CYP76AH3 at 3.67 Angstroms resolution Authors: Chang, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x2q.cif.gz | 398.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x2q.ent.gz | 310.8 KB | Display | PDB format |
PDBx/mmJSON format | 7x2q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7x2q_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7x2q_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7x2q_validation.xml.gz | 36.5 KB | Display | |
Data in CIF | 7x2q_validation.cif.gz | 47.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/7x2q ftp://data.pdbj.org/pub/pdb/validation_reports/x2/7x2q | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 53659.051 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salvia miltiorrhiza (Chinese salvia) / Gene: CYP76AH3 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0Y0GRS3, sugiol synthase, ferruginol monooxygenase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.94 % |
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Crystal grow | Temperature: 289.1 K / Method: vapor diffusion / Details: 1600mmol/L sodium citrate tribasic |
-Data collection
Diffraction | Mean temperature: 193.1 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97853 Å |
Detector | Type: Brandeis B4 / Detector: CCD / Date: May 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 3.67→39.23 Å / Num. obs: 11668 / % possible obs: 96.8 % / Redundancy: 35.5 % / Biso Wilson estimate: 67.16 Å2 / Rpim(I) all: 0.064 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 3.67→4.04 Å / Num. unique obs: 11620 / CC1/2: 0.741 |
Serial crystallography sample delivery | Method: fixed target |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.68→39.23 Å / SU ML: 0.4803 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 36.9293 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.99 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.68→39.23 Å
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Refine LS restraints |
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LS refinement shell |
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