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Yorodumi- PDB-2e91: S. cerevisiae geranylgeranyl pyrophosphate synthase in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2.0E+91 | ||||||
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Title | S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium and BPH-91 | ||||||
Components | Geranylgeranyl pyrophosphate synthetase | ||||||
Keywords | TRANSFERASE / prenyltransferase / farnesyl pyrophosphate / bisphosphonate | ||||||
Function / homology | Function and homology information Cholesterol biosynthesis / plastoquinone biosynthetic process / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / transferase complex / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / prenyltransferase activity ...Cholesterol biosynthesis / plastoquinone biosynthetic process / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / transferase complex / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / prenyltransferase activity / farnesyltranstransferase activity / ubiquinone biosynthetic process / terpenoid biosynthetic process / isoprenoid biosynthetic process / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / protein transport / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||
Authors | Guo, R.T. / Ko, T.P. / Cao, R. / 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 | 2e91.cif.gz | 141.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e91.ent.gz | 109.9 KB | Display | PDB format |
PDBx/mmJSON format | 2e91.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2e91_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2e91_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2e91_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 2e91_validation.cif.gz | 42.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/2e91 ftp://data.pdbj.org/pub/pdb/validation_reports/e9/2e91 | HTTPS FTP |
-Related structure data
Related structure data | 2e8tC 2e8uC 2e8vC 2e8wC 2e8xC 2e90C 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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-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: 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: 2.19 Å3/Da / Density % sol: 43.84 % |
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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 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / 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: 2.14→30 Å / Num. all: 38999 / Num. obs: 38804 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Redundancy: 6.33 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 2.14→2.22 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 4.6 / Num. unique all: 3795 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DH4 Resolution: 2.14→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 43.23 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.24 Å / Luzzati sigma a obs: 0.19 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.14→2.22 Å
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