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- PDB-3rmg: Crystal structure of geranylgeranyl pyrophosphate synthase from b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3rmg | ||||||
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Title | Crystal structure of geranylgeranyl pyrophosphate synthase from bacteroides thetaiotaomicron | ||||||
![]() | Octaprenyl-diphosphate synthase | ||||||
![]() | TRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / ISOPRENE BIOSYNTHESIS / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / NYSGXRC / ENZYME FUNCTION INITIATIVE / EFI / PSI-2 | ||||||
Function / homology | ![]() prenyltransferase activity / isoprenoid biosynthetic process / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Patskovsky, Y. / Toro, R. / Sauder, J.M. / Poulter, C.D. / Gerlt, J.A. / Burley, S.K. / Almo, S.C. / Enzyme Function Initiative (EFI) / 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 | ![]() | 125.3 KB | Display | ![]() |
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PDB format | ![]() | 98.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3lomC ![]() 3lvsC ![]() 3mzvC ![]() 3nf2C ![]() 3oyrC ![]() 3p41C ![]() 3p8lC ![]() 3p8rC ![]() 3pdeC ![]() 3pkoC ![]() 3q1oC ![]() 3q2qC ![]() 3qqvC ![]() 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 0 - 322 / Label seq-ID: 3 - 324
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Components
#1: Protein | Mass: 37066.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: VPI-5482 / Gene: BT_3261 / Plasmid: BC-PSGX3(BC) / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.2 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7 Details: 0.15M MALIC ACID, PH 7.0, 30% PEG 3350, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2010 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 41607 / % possible obs: 99.9 % / Observed criterion σ(I): -5 / Redundancy: 4.2 % / Biso Wilson estimate: 46.037 Å2 / Rsym value: 0.07 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.598 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2128 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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