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Yorodumi- PDB-3zou: Native structure of Farnesyl Pyrophosphate Synthase from Pseudomo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zou | ||||||
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Title | Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PA01, with bound fragment SPB02696, and substrate geranyl pyrophosphate. | ||||||
Components | FARNESYL PYROPHOSPHATE SYNTHASEDimethylallyltranstransferase | ||||||
Keywords | TRANSFERASE / PA4043 | ||||||
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: 1.55 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 | 3zou.cif.gz | 134.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zou.ent.gz | 103.6 KB | Display | PDB format |
PDBx/mmJSON format | 3zou.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/3zou ftp://data.pdbj.org/pub/pdb/validation_reports/zo/3zou | HTTPS FTP |
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-Related structure data
Related structure data | 3zcdSC 3zl6C 3zmbC 3zmcC 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: (-0.2147, -0.9648, -0.152), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 6 types, 583 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-GPP / | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-DMS / | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | 3-(2-OXO-1,3-BENZOXAZOLSequence 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: 2.03 Å3/Da / Density % sol: 39.34 % Description: DATA WAS REFINED AGAINST PA4043 NATIVE MODEL 3ZCD. |
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Crystal grow | pH: 8 Details: 15% GLYCEROL, 0.2 M MGCL2, 20% PEG6000, 0.1 M TRIS PH 8, 0.274 MM GPP, 10 MM SPB02696, 10% METHANOL, 1% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 9, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→30.67 Å / Num. obs: 77089 / % possible obs: 96.9 % / Observed criterion σ(I): 1.9 / Redundancy: 4.2 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.9 / % possible all: 75.8 |
-Processing
Software |
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Refinement | Method to determine structure: SIR Starting model: PDB ENTRY 3ZCD Resolution: 1.55→30.69 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.389 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.08 / 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: 18.751 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→30.69 Å
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Refine LS restraints |
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