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Yorodumi- PDB-2z7h: S. cerevisiae geranylgeranyl pyrophosphate synthase in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z7h | ||||||
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Title | S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with inhibitor BPH-210 | ||||||
Components | Geranylgeranyl pyrophosphate synthetase | ||||||
Keywords | TRANSFERASE / prenyltransferase / geranylgeranyl pyrophosphate / bisphosphonate / Carotenoid biosynthesis / Cytoplasm / Isoprene biosynthesis / Multifunctional enzyme / Protein transport / Transport | ||||||
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: 2.08 Å | ||||||
Authors | Cao, R. / Chen, C.K.-M. / Guo, R.-T. / Hudock, M. / Wang, A.H.-J. / Oldfield, E. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Structures of a potent phenylalkyl bisphosphonate inhibitor bound to farnesyl and geranylgeranyl diphosphate synthases. Authors: Cao, R. / Chen, C.K. / Guo, R.T. / Wang, A.H. / Oldfield, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z7h.cif.gz | 151.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z7h.ent.gz | 117.2 KB | Display | PDB format |
PDBx/mmJSON format | 2z7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/2z7h ftp://data.pdbj.org/pub/pdb/validation_reports/z7/2z7h | HTTPS FTP |
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-Related structure data
Related structure data | 2p1cC 2dh4S 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 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q12051, heptaprenyl diphosphate synthase, dimethylallyltranstransferase, (2E,6E)-farnesyl diphosphate synthase, geranylgeranyl 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: 2.24 Å3/Da / Density % sol: 45.19 % |
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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: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2007 / 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: 2.08→30 Å / Num. all: 77404 / Num. obs: 43398 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 30.9 |
Reflection shell | Resolution: 2.08→2.15 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 5.3 / Num. unique all: 7152 / % possible all: 89.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DH4 Resolution: 2.08→24.8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 45.75 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.24 Å / Luzzati sigma a obs: 0.24 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→24.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.08→2.15 Å
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