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- PDB-4pvy: Crystal structure of human FPPS in complex with [({5-[4-(propan-2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pvy | ||||||
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Title | Crystal structure of human FPPS in complex with [({5-[4-(propan-2-yloxy)phenyl]pyridin-3-yl}amino)methanediyl]bis(phosphonic acid) | ||||||
![]() | Farnesyl pyrophosphate synthase | ||||||
![]() | Transferase/transferase inhibitor / Transferase-transferase inhibitor complex | ||||||
Function / homology | ![]() geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding / nucleoplasm / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Rodionov, D. / Park, J. / De Schutter, J.W. / Tsantrizos, Y.S. / Berghuis, A.M. | ||||||
![]() | ![]() Title: Crystallographic and thermodynamic characterization of phenylaminopyridine bisphosphonates binding to human farnesyl pyrophosphate synthase. Authors: Park, J. / Rodionov, D. / De Schutter, J.W. / Lin, Y.S. / Tsantrizos, Y.S. / Berghuis, A.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.1 KB | Display | ![]() |
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PDB format | ![]() | 128.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 707.4 KB | Display | ![]() |
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Full document | ![]() | 709 KB | Display | |
Data in XML | ![]() | 17.1 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nfiC ![]() 4nfjC ![]() 4nfkC ![]() 4pvxC ![]() 4h5cS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 43144.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P14324, (2E,6E)-farnesyl diphosphate synthase, dimethylallyltranstransferase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-JD1 / [({ | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.65 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.7M sodium chloride, 15% glycerol, 0.085M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 10, 2014 / Details: Rigaku Varimax-HF |
Radiation | Monochromator: Rigaku Varimax-HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→111.06 Å / Num. all: 26578 / Num. obs: 26578 / % possible obs: 98.8 % / Redundancy: 32.9 % / Biso Wilson estimate: 22.614 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 44.1 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 3 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1769 / % possible all: 90.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4H5C Resolution: 2.05→111.06 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.672 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.151 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.252 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→111.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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