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- PDB-3mzv: Crystal structure of a decaprenyl diphosphate synthase from Rhodo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mzv | ||||||
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Title | Crystal structure of a decaprenyl diphosphate synthase from Rhodobacter capsulatus | ||||||
![]() | Decaprenyl diphosphate synthase | ||||||
![]() | TRANSFERASE / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Quartararo, C.E. / Patskovsky, Y. / Bonanno, J.B. / Rutter, M. / Bain, K.T. / Chang, S. / Toro, R. / Sauder, J.M. / Burley, S.K. / 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 | ![]() | 252.7 KB | Display | ![]() |
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PDB format | ![]() | 206.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.1 KB | Display | ![]() |
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Full document | ![]() | 447.4 KB | Display | |
Data in XML | ![]() | 27.2 KB | Display | |
Data in CIF | ![]() | 39.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lomC ![]() 3lvsC ![]() 3nf2C ![]() 3oyrC ![]() 3p41C ![]() 3p8lC ![]() 3p8rC ![]() 3pdeC ![]() 3pkoC ![]() 3q1oC ![]() 3q2qC ![]() 3qqvC ![]() 3rmgC ![]() 3ts7C ![]() 3ucaC ![]() 4dhdC ![]() 4f62C ![]() 4fp4C 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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Unit cell |
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Components
#1: Protein | Mass: 37480.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.11 % |
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Crystal grow | Temperature: 294 K / pH: 6.5 Details: 100mM MES pH 6.5, 30% PEG MME 5K, 200mM ammonium sulfate, vapor diffusion, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 26, 2010 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97958 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 56604 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 3 / Rsym value: 0.479 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
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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: 46.95 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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