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Yorodumi- PDB-3zl6: Native structure of Farnesyl Pyrophosphate Synthase from Pseudomo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zl6 | ||||||
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Title | Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PAO1, with bound fragment KM10833. | ||||||
Components | GERANYLTRANSTRANSFERASE | ||||||
Keywords | TRANSFERASE / KM10833 / MAYBRIDGE FRAGMENT LIBRARY | ||||||
Function / homology | Function and homology information prenyltransferase activity / isoprenoid biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR / 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 | 3zl6.cif.gz | 125.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zl6.ent.gz | 97.3 KB | Display | PDB format |
PDBx/mmJSON format | 3zl6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/3zl6 ftp://data.pdbj.org/pub/pdb/validation_reports/zl/3zl6 | HTTPS FTP |
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-Related structure data
Related structure data | 3zcdSC 3zmbC 3zmcC 3zouC 4umjC 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.2177, -0.9637, -0.1544), Vector: |
-Components
#1: Protein | Mass: 31588.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: Q9HWY4, (2E,6E)-farnesyl diphosphate synthase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | (1,2-BENZISOXAZ | Sequence details | THERE IS AN N-TERMINAL ADDITIONAL | |
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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: 2.31 Å3/Da / Density % sol: 46.7 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 0.2 M MGCL2, 20% PEG6000, 0.1 M TRISCL PH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1.00319 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 10, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00319 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→32.26 Å / Num. obs: 47364 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SIR Starting model: PDB ENTRY 3ZCD Resolution: 1.85→31.35 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.929 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.134 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.21 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→31.35 Å
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Refine LS restraints |
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