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- PDB-3p41: Crystal structure of polyprenyl synthetase from pseudomonas fluor... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3p41 | ||||||
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Title | Crystal structure of polyprenyl synthetase from pseudomonas fluorescens pf-5 complexed with magnesium and isoprenyl pyrophosphate | ||||||
![]() | Geranyltranstransferase | ||||||
![]() | TRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / ISOPRENE BIOSYNTHESIS / PSI-2 / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS | ||||||
Function / homology | ![]() (2E,6E)-farnesyl diphosphate synthase / isoprenoid biosynthetic process / geranyltranstransferase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Patskovsky, Y. / Toro, R. / Sauder, J.M. / Burley, S.K. / Poulter, C.D. / Gerlt, J.A. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.5 KB | Display | ![]() |
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PDB format | ![]() | 57 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.8 KB | Display | ![]() |
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Full document | ![]() | 473.5 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lomC ![]() 3lvsC ![]() 3mzvC ![]() 3nf2C ![]() 3oyrC ![]() 3p8lC ![]() 3p8rC ![]() 3pdeC ![]() 3pkoC ![]() 3q1oC ![]() 3q2qC ![]() 3qqvC ![]() 3rmgC ![]() 3ts7C ![]() 3ucaC ![]() 4dhdC ![]() 4f62C ![]() 4fp4C ![]() 3ljiS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 32836.988 Da / Num. of mol.: 1 / Fragment: sequence database residues 3-295 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 150 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/DMA.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMA.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-POP / | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.65 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M SODIUM CACODYLATE, PH 6.5, 20% PEG 8K, 200MM MAGNESIUM ACETATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→40 Å / Num. obs: 29256 / % possible obs: 97.2 % / Observed criterion σ(I): -5 / Redundancy: 5.2 % / Biso Wilson estimate: 23.078 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 1.76→1.79 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.5 / % possible all: 78.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3LJI Resolution: 1.76→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.395 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.119 / 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: 34.746 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.805 Å / Total num. of bins used: 20
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