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Yorodumi- PDB-3pde: Crystal structure of geranylgeranyl pyrophosphate synthase from L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pde | ||||||
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Title | Crystal structure of geranylgeranyl pyrophosphate synthase from Lactobacillus brevis atcc 367 complexed with isoprenyl diphosphate and magnesium | ||||||
Components | Farnesyl-diphosphate synthase | ||||||
Keywords | TRANSFERASE / ISOPRENYL DIPHOSPHATE SYNTHASE / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / ISOPRENE BIOSYNTHESIS / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS | ||||||
Function / homology | Function and homology information farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity Similarity search - Function | ||||||
Biological species | Lactobacillus brevis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Patskovsky, Y. / Toro, R. / Rutter, M. / Sauder, J.M. / Burley, S.K. / Poulter, C.D. / Gerlt, J.A. / 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 | 3pde.cif.gz | 256.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pde.ent.gz | 204.6 KB | Display | PDB format |
PDBx/mmJSON format | 3pde.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/3pde ftp://data.pdbj.org/pub/pdb/validation_reports/pd/3pde | HTTPS FTP |
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-Related structure data
Related structure data | 3lomC 3lvsC 3mzvC 3nf2C 3oyrC 3p41C 3p8lC 3p8rC 3pkoC 3q1oC 3q2qC 3qqvC 3rmgC 3ts7C 3ucaC 4dhdC 4f62C 4fp4C 3m9uS S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33341.824 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus brevis (bacteria) / Strain: ATCC 367 / JCM 1170 / Gene: LVIS_0975 / Production host: Escherichia coli (E. coli) References: UniProt: Q03RR4, (2E,6E)-farnesyl diphosphate synthase #2: Chemical | ChemComp-DMA / #3: Chemical | ChemComp-MG / #4: Chemical | #5: 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: 2.25 Å3/Da / Density % sol: 45.42 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1M SODIUM ACETATE, PH 4.5, 25% PEG3350, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2010 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→40 Å / Num. obs: 118339 / % possible obs: 97 % / Observed criterion σ(I): -5 / Redundancy: 2.4 % / Biso Wilson estimate: 20.784 Å2 / Rsym value: 0.085 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.3 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3M9U Resolution: 1.75→40 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.314 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.109 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.018 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.747→1.792 Å / Total num. of bins used: 20
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