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Yorodumi- PDB-4ee8: Crystal structure of the Novel Phenazine Prenyltransferase EpzP (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ee8 | ||||||
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Title | Crystal structure of the Novel Phenazine Prenyltransferase EpzP (wildtype) | ||||||
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 / ACETATE ION / Prenyltransferase Function and homology information | ||||||
Biological species | Streptomyces cinnamonensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / PHASER / Resolution: 1.93 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 | 4ee8.cif.gz | 135.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ee8.ent.gz | 104.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ee8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ee8_validation.pdf.gz | 452.8 KB | Display | wwPDB validaton report |
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Full document | 4ee8_full_validation.pdf.gz | 453.7 KB | Display | |
Data in XML | 4ee8_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 4ee8_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/4ee8 ftp://data.pdbj.org/pub/pdb/validation_reports/ee/4ee8 | HTTPS FTP |
-Related structure data
Related structure data | 4ee6C 4ee7C 2xlqS C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33413.871 Da / Num. of mol.: 1 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, 249 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-EPE / | #6: 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: 2.98 Å3/Da / Density % sol: 58.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2.4 M (NH4)2SO4, 100 mM HEPES/NaOH pH 7.5, 200 mM sodium acetate, 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: Aug 16, 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: 1.93→30 Å / Num. obs: 30684 / % possible obs: 98.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.93→1.98 Å / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: PHASER Starting model: PDB ENTRY 2XLQ Resolution: 1.93→28.61 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.078 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.117 / 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: 25.754 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→28.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.98 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 4.8696 Å / Origin y: 18.7663 Å / Origin z: 16.8083 Å
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