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Yorodumi- PDB-3rmg: Crystal structure of geranylgeranyl pyrophosphate synthase from b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rmg | ||||||
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Title | Crystal structure of geranylgeranyl pyrophosphate synthase from bacteroides thetaiotaomicron | ||||||
Components | Octaprenyl-diphosphate synthase | ||||||
Keywords | 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 | Function and homology information prenyltransferase activity / isoprenoid biosynthetic process / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | 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) | ||||||
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 | 3rmg.cif.gz | 125.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rmg.ent.gz | 98.8 KB | Display | PDB format |
PDBx/mmJSON format | 3rmg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rm/3rmg ftp://data.pdbj.org/pub/pdb/validation_reports/rm/3rmg | 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 (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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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.) Bacteroides thetaiotaomicron (bacteria) Strain: VPI-5482 / Gene: BT_3261 / Plasmid: BC-PSGX3(BC) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q8A2P4 #2: 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: 2.81 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: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.162 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.219 / 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: 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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