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Yorodumi- PDB-4umj: Native structure of Farnesyl Pyrophosphate Synthase from Pseudomo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4umj | ||||||
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Title | Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PA01, with bound ibandronic acid molecules. | ||||||
Components | GERANYLTRANSTRANSFERASE | ||||||
Keywords | TRANSFERASE / FPPS / BONVIVA / BISPHOSPHONATE | ||||||
Function / homology | Function and homology information prenyltransferase activity / isoprenoid biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.85 Å | ||||||
Authors | Schmidberger, J.W. / Schnell, R. / Schneider, G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Structural Characterization of Substrate and Inhibitor Binding to Farnesyl Pyrophosphate Synthase from Pseudomonas Aeruginosa. Authors: Schmidberger, J.W. / Schnell, R. / Schneider, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4umj.cif.gz | 131.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4umj.ent.gz | 103.1 KB | Display | PDB format |
PDBx/mmJSON format | 4umj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4umj_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 4umj_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4umj_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 4umj_validation.cif.gz | 43.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/4umj ftp://data.pdbj.org/pub/pdb/validation_reports/um/4umj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 31588.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PA01 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9HWY4, (2E,6E)-farnesyl diphosphate synthase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-BFQ / #4: Water | ChemComp-HOH / | Nonpolymer details | 7-[2, 6-DICHLORO-4-({[(2-CHLOROBENZ | Sequence details | THERE IS AN EXTRA SERINE AT THE N-TERMINUS FROM CLONING. | |
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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: 2.4 Å3/Da / Density % sol: 49 % Description: THE DATA REPRESENTED A COMPOUND SOAK. DATA WAS REFINED AGAINST EXISTING MODEL. 3ZCD |
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Crystal grow | pH: 8 / Details: 0.2 M MGCL2, 20% PEG6000, 0.1 M TRIS CL PH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Type: ESRF / Wavelength: 0.9801 |
Detector | Date: Jul 7, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→65.67 Å / Num. obs: 46925 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.8 / % possible all: 94.5 |
-Processing
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.85→65.66 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.133 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES, REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.98 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→65.66 Å
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