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- PDB-2zev: S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zev | ||||||
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Title | S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium, IPP and BPH-715 | ||||||
![]() | Geranylgeranyl pyrophosphate synthetase | ||||||
![]() | TRANSFERASE / PRENYLTRANSFERASE / FARNESYL PYROPHOSPHATE / BISPHOSPHONATE / Carotenoid biosynthesis / Isoprene biosynthesis / Multifunctional enzyme / Protein transport / Transport | ||||||
Function / homology | ![]() Cholesterol biosynthesis / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / prenyltransferase activity / farnesyltranstransferase activity / terpenoid biosynthetic process ...Cholesterol biosynthesis / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / prenyltransferase activity / farnesyltranstransferase activity / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guo, R.T. / Chen, C.K.-M. / Cao, R. / Oldfield, E. / Wang, A.H.-J. | ||||||
![]() | ![]() Title: Lipophilic bisphosphonates as dual farnesyl/geranylgeranyl diphosphate synthase inhibitors: an X-ray and NMR investigation Authors: Zhang, Y. / Cao, R. / Yin, F. / Hudock, M.P. / Guo, R.T. / Krysiak, K. / Mukherjee, S. / Gao, Y.-G. / Robinson, H. / Song, Y. / No, J.H. / Bergan, K. / Leon, A. / Cass, L. / Goddard, A. / ...Authors: Zhang, Y. / Cao, R. / Yin, F. / Hudock, M.P. / Guo, R.T. / Krysiak, K. / Mukherjee, S. / Gao, Y.-G. / Robinson, H. / Song, Y. / No, J.H. / Bergan, K. / Leon, A. / Cass, L. / Goddard, A. / Chang, T.-K. / Lin, F.-Y. / Van Beek, E. / Papapoulos, S. / Wang, A.H.-J. / Kubo, T. / Ochi, M. / Mukkamala, D. / Oldfield, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.3 KB | Display | ![]() |
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PDB format | ![]() | 113.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2opmC ![]() 2zeuC ![]() 3dyfC ![]() 3dygC ![]() 3dyhC ![]() 3efqC ![]() 3egtC ![]() 2dh4S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Plasmid: PET32/LIC / Production host: ![]() ![]() References: UniProt: Q12051, heptaprenyl diphosphate synthase #2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | ChemComp-IPE / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.62 % |
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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 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / 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: 2.23→50 Å / Num. all: 35636 / Num. obs: 33587 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 41.3 |
Reflection shell | Resolution: 2.23→2.31 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3069 / % possible all: 86.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2DH4 Resolution: 2.23→41.81 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: 48.64 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.26 Å / Luzzati sigma a obs: 0.24 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.23→41.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.23→2.31 Å
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