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Yorodumi- PDB-7fhc: Structure of prenyltransferase mutant V49W from Streptomyces sp. ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fhc | ||||||
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Title | Structure of prenyltransferase mutant V49W from Streptomyces sp. (strain CL190) | ||||||
Components | Prenyltransferase | ||||||
Keywords | TRANSFERASE / PT-barrel | ||||||
Function / homology | Aromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / prenyltransferase activity / metal ion binding / Prenyltransferase Function and homology information | ||||||
Biological species | Streptomyces sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.06 Å | ||||||
Authors | Xue, B. / Lim, K.J.H. / Hartono, Y.D. / Go, M.D.K. / Fan, H. / Yew, W.S. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: Acs Catalysis / Year: 2022 Title: Structure-Guided Engineering of Prenyltransferase NphB for High-Yield and Regioselective Cannabinoid Production. Authors: Lim, K.J.H. / Hartono, Y.D. / Xue, B. / Go, M.K. / Fan, H. / Yew, W.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fhc.cif.gz | 78 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fhc.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 7fhc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fhc_validation.pdf.gz | 418.5 KB | Display | wwPDB validaton report |
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Full document | 7fhc_full_validation.pdf.gz | 419.7 KB | Display | |
Data in XML | 7fhc_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 7fhc_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/7fhc ftp://data.pdbj.org/pub/pdb/validation_reports/fh/7fhc | HTTPS FTP |
-Related structure data
Related structure data | 7fhbC 7fhdC 7fheC 7fhfC 1zb6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34019.441 Da / Num. of mol.: 1 / Mutation: V49W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. (strain CL190) (bacteria) Strain: CL190 / Plasmid: pSY5CDF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4R2T2 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % / Mosaicity: 0.07 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.0, 18% w/v PEG 20,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→44.34 Å / Num. obs: 19285 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 21.32 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.34 / Rpim(I) all: 0.097 / Rrim(I) all: 0.354 / Net I/σ(I): 6.9 / Num. measured all: 252772 / Scaling rejects: 468 |
Reflection shell | Resolution: 2.06→2.11 Å / Redundancy: 12.6 % / Rmerge(I) obs: 1.842 / Num. unique obs: 1457 / CC1/2: 0.683 / Rpim(I) all: 0.528 / Rrim(I) all: 1.919 / % possible all: 98.7 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZB6 Resolution: 2.06→42.8 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.45 / Stereochemistry target values: ML
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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 max: 65.35 Å2 / Biso mean: 22.0201 Å2 / Biso min: 9.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.06→42.8 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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