+Open data
-Basic information
Entry | Database: PDB / ID: 5uco | ||||||
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Title | Benzophenone synthase from Hypericum androsaemum | ||||||
Components | 2,4,6-trihydroxybenzophenone synthase | ||||||
Keywords | TRANSFERASE / thiolase / polyketide / benzoyl-CoA | ||||||
Function / homology | Function and homology information 2,3',4,6-tetrahydroxybenzophenone synthase / 2,4,6-trihydroxybenzophenone synthase / tetrahydroxybenzophenone synthase activity / trihydroxybenzophenone synthase activity / benzoyl-CoA metabolic process / malonyl-CoA metabolic process / biosynthetic process / acyltransferase activity Similarity search - Function | ||||||
Biological species | Hypericum androsaemum (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å | ||||||
Authors | Stewart Jr, C.E. / Noel, J.P. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2017 Title: Molecular architectures of benzoic acid-specific type III polyketide synthases. Authors: Stewart, C. / Woods, K. / Macias, G. / Allan, A.C. / Hellens, R.P. / Noel, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uco.cif.gz | 271.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uco.ent.gz | 220.8 KB | Display | PDB format |
PDBx/mmJSON format | 5uco.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uco_validation.pdf.gz | 424.9 KB | Display | wwPDB validaton report |
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Full document | 5uco_full_validation.pdf.gz | 426 KB | Display | |
Data in XML | 5uco_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 5uco_validation.cif.gz | 35.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/5uco ftp://data.pdbj.org/pub/pdb/validation_reports/uc/5uco | HTTPS FTP |
-Related structure data
Related structure data | 5uc5C 5w8qC 5wc4C 1bi5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43017.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: codon optimized for E.coli expression, His-tag removed after purification Source: (gene. exp.) Hypericum androsaemum (plant) / Gene: BPS / Plasmid: pHIS8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8SAS8, 2,3',4,6-tetrahydroxybenzophenone synthase #2: Water | ChemComp-HOH / | |
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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: 2.72 Å3/Da / Density % sol: 54.79 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Reservoir: PIPES (pH 6.5) 100mM, PEG8000 18%; ratio of protein to reservoir = 1:1 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2013 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.85→184.97 Å / Num. all: 18840 / Num. obs: 18840 / % possible obs: 85 % / Redundancy: 3.5 % / Biso Wilson estimate: 21.7 Å2 / Rpim(I) all: 0.142 / Rrim(I) all: 0.294 / Rsym value: 0.253 / Net I/av σ(I): 2.2 / Net I/σ(I): 4.5 / Num. measured all: 65535 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BI5 Resolution: 2.85→46.242 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.09
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.38 Å2 / Biso mean: 15.6359 Å2 / Biso min: 2.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.85→46.242 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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