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Yorodumi- PDB-2e8t: S. cerevisiae geranylgeranyl pyrophosphate synthase in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e8t | ||||||
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Title | S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium, FsPP and IPP | ||||||
Components | Geranylgeranyl pyrophosphate synthetase | ||||||
Keywords | TRANSFERASE / prenyltransferase / farnesyl pyrophosphate / bisphosphonate | ||||||
Function / homology | Function and homology information Cholesterol biosynthesis / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / farnesyltranstransferase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity ...Cholesterol biosynthesis / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / farnesyltranstransferase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / prenyltransferase activity / dimethylallyltranstransferase activity / terpenoid biosynthetic process / isoprenoid biosynthetic process / protein transport / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Guo, R.T. / Ko, T.P. / Chen, C.K.-M. / Jeng, W.Y. / Chang, T.H. / Liang, P.H. / Oldfield, E. / Wang, A.H.-J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Bisphosphonates target multiple sites in both cis- and trans-prenyltransferases Authors: Guo, R.T. / Cao, R. / Liang, P.H. / Ko, T.P. / Chang, T.H. / Hudock, M.P. / Jeng, W.Y. / Chen, C.K.-M. / Zhang, Y. / Song, Y. / Kuo, C.J. / Yin, F. / Oldfield, E. / Wang, A.H.-J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e8t.cif.gz | 148.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e8t.ent.gz | 115.6 KB | Display | PDB format |
PDBx/mmJSON format | 2e8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/2e8t ftp://data.pdbj.org/pub/pdb/validation_reports/e8/2e8t | HTTPS FTP |
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-Related structure data
Related structure data | 2e8uC 2e8vC 2e8wC 2e8xC 2e90C 2e91C 2e92C 2e93C 2e94C 2e95C 2e98C 2e99C 2e9aC 2e9cC 2e9dC 2dh4S 2e96 2e97 S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer. |
-Components
#1: Protein | Mass: 39299.059 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pET32/LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: Q12051, heptaprenyl diphosphate synthase #2: Chemical | ChemComp-MG / #3: Chemical | #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: 2.24 Å3/Da / Density % sol: 45.17 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.08M CH3COONa, 16% PEG 4000, 6-10% glycerol, 6-10% 1,2-propanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→50 Å / Num. all: 41038 / Num. obs: 39107 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.57 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 28.9 |
Reflection shell | Resolution: 2.13→2.21 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 5.1 / Num. unique all: 3249 / % possible all: 81.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DH4 Resolution: 2.13→30.9 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 43.72 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.24 Å / Luzzati sigma a obs: 0.2 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→30.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.13→2.21 Å
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