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Yorodumi- PDB-3lvs: Crystal structure of farnesyl diphosphate synthase from rhodobact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lvs | ||||||
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Title | Crystal structure of farnesyl diphosphate synthase from rhodobacter capsulatus sb1003 | ||||||
Components | FARNESYL DIPHOSPHATE SYNTHASE | ||||||
Keywords | TRANSFERASE / ISOPRENYL DIPHOSPHATE SYNTHASE / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / NYSGRC / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information farnesyl diphosphate biosynthetic process / geranyltranstransferase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodobacter capsulatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å | ||||||
Authors | Patskovsky, Y. / Toro, R. / Rutter, M. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily. Authors: Wallrapp, F.H. / Pan, J.J. / Ramamoorthy, G. / Almonacid, D.E. / Hillerich, B.S. / Seidel, R. / Patskovsky, Y. / Babbitt, P.C. / Almo, S.C. / Jacobson, M.P. / Poulter, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lvs.cif.gz | 113 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lvs.ent.gz | 87.1 KB | Display | PDB format |
PDBx/mmJSON format | 3lvs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/3lvs ftp://data.pdbj.org/pub/pdb/validation_reports/lv/3lvs | HTTPS FTP |
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-Related structure data
Related structure data | 3lomC 3mzvC 3nf2C 3oyrC 3p41C 3p8lC 3p8rC 3pdeC 3pkoC 3q1oC 3q2qC 3qqvC 3rmgC 3ts7C 3ucaC 4dhdC 4f62C 4fp4C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31001.178 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Strain: ATCC BAA-309D / Gene: Trans_IPPS_HT / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KWR7*PLUS #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: 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: 2.62 Å3/Da / Density % sol: 53.12 % / Description: DATA ANISOTROPIC |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG8000, 50MM POTASSIUM DIHYDROGEN PHOSPHATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 23, 2010 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→40 Å / Num. obs: 36089 / % possible obs: 99.8 % / Observed criterion σ(I): -5 / Redundancy: 3.4 % / Biso Wilson estimate: 43.86 Å2 / Rsym value: 0.085 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 0.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.113 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.187 / 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: 61.882 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.205 Å / Total num. of bins used: 20
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