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Yorodumi- PDB-4ee7: Crystal Structure of the Novel Phenazine Prenyltransferase EpzP i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ee7 | ||||||
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Title | Crystal Structure of the Novel Phenazine Prenyltransferase EpzP in complex with S-thiolodiphosphate (methylated) | ||||||
Components | Prenyltransferase | ||||||
Keywords | TRANSFERASE / PT fold / dihydrophenazine carboxylate prenyltransferase | ||||||
Function / homology | Aromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / prenyltransferase activity / metabolic process / TRIHYDROGEN THIODIPHOSPHATE / Prenyltransferase Function and homology information | ||||||
Biological species | Streptomyces cinnamonensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / PHASER / Resolution: 1.67 Å | ||||||
Authors | Zocher, G. / Stehle, T. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Structure-based engineering increased the catalytic turnover rate of a novel phenazine prenyltransferase. Authors: Zocher, G. / Saleh, O. / Heim, J.B. / Herbst, D.A. / Heide, L. / Stehle, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ee7.cif.gz | 243.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ee7.ent.gz | 205.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ee7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/4ee7 ftp://data.pdbj.org/pub/pdb/validation_reports/ee/4ee7 | HTTPS FTP |
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-Related structure data
-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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 33549.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces cinnamonensis (bacteria) / Gene: epzP / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: E5KWG9 |
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-Non-polymers , 5 types, 646 molecules
#2: Chemical | ChemComp-PIS / | ||||||
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#3: Chemical | ChemComp-PG4 / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-CL / | #6: 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: 2.07 Å3/Da / Density % sol: 40.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 200 mM (NH4)2SO4, 30% (w/v) PEG2000MME, 100 mM sodium acetate 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 7, 2010 |
Radiation | Monochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→30 Å / Num. all: 65578 / Num. obs: 65469 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.67→1.71 Å / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: PHASER / Resolution: 1.67→29.39 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.287 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.188 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→29.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.67→1.713 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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