+Open data
-Basic information
Entry | Database: PDB / ID: 5x9j | ||||||
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Title | Structure of PrhC from Penicillium brasilianum NBRC 6234 | ||||||
Components | PrhC | ||||||
Keywords | ISOMERASE / meroterpenoid / paraherquonin | ||||||
Function / homology | paraherquonin biosynthetic process / : / Isomerases / isomerase activity / Isomerase prhC Function and homology information | ||||||
Biological species | Penicillium brasilianum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Mori, T. / Wang, H. / Matsuda, Y. / Abe, I. | ||||||
Citation | Journal: Nat. Chem. Biol. / Year: 2017 Title: Molecular basis for the unusual ring reconstruction in fungal meroterpenoid biogenesis Authors: Mori, T. / Iwabuchi, T. / Hoshino, S. / Wang, H. / Matsuda, Y. / Abe, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x9j.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x9j.ent.gz | 56 KB | Display | PDB format |
PDBx/mmJSON format | 5x9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x9j_validation.pdf.gz | 429.2 KB | Display | wwPDB validaton report |
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Full document | 5x9j_full_validation.pdf.gz | 429.9 KB | Display | |
Data in XML | 5x9j_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 5x9j_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/5x9j ftp://data.pdbj.org/pub/pdb/validation_reports/x9/5x9j | HTTPS FTP |
-Related structure data
Related structure data | 5wqfSC 5wqgC 5wqhC 5wqiC 5x9kC 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: 21454.053 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Penicillium brasilianum (fungus) / Gene: prhC / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E1FFL1 #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: 4.13 Å3/Da / Density % sol: 70.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100mM HEPES (pH 7.5), 1.125M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→50 Å / Num. obs: 41556 / % possible obs: 99.9 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 22.19 |
Reflection shell | Resolution: 2.09→2.22 Å / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 4.35 / Num. unique obs: 6597 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WQF Resolution: 2.1→46.695 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.95
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.695 Å
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Refine LS restraints |
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LS refinement shell |
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