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Yorodumi- PDB-3zmc: Native structure of Farnesyl Pyrophosphate Synthase from Pseudomo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zmc | ||||||
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Title | Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PA01, with bound substrate molecule Geranyl pyrophosphate. | ||||||
Components | GERANYLTRANSTRANSFERASE | ||||||
Keywords | TRANSFERASE | ||||||
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: 1.87 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 | 3zmc.cif.gz | 126.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zmc.ent.gz | 97.8 KB | Display | PDB format |
PDBx/mmJSON format | 3zmc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zmc_validation.pdf.gz | 951.8 KB | Display | wwPDB validaton report |
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Full document | 3zmc_full_validation.pdf.gz | 962.5 KB | Display | |
Data in XML | 3zmc_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 3zmc_validation.cif.gz | 37.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/3zmc ftp://data.pdbj.org/pub/pdb/validation_reports/zm/3zmc | HTTPS FTP |
-Related structure data
Related structure data | 3zcdSC 3zl6C 3zmbC 3zouC 4umjC 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.2188, -0.9655, -0.1415), 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 , 5 types, 425 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-DMS / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.21 Å3/Da / Density % sol: 44.28 % Description: DATA IS SUBSTRATE COMPLEX, SOLVED BY REFINING AGAINST NATIVE MODEL USING NATIVE FREER FLAGS. |
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Crystal grow | pH: 8 / Details: 0.15 M MGCL2, 20% PEG8000, 0.1 M TRISCL PH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97626 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 29, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→40.83 Å / Num. obs: 46143 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.87→1.91 Å / Redundancy: 5 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SIR Starting model: PDB ENTRY 3ZCD Resolution: 1.87→40.86 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.889 / SU B: 3.581 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.154 / 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: 20.409 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→40.86 Å
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Refine LS restraints |
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