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- PDB-4nfj: Crystal structure of human FPPS in complex with magnesium, JDS051... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4nfj | ||||||
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Title | Crystal structure of human FPPS in complex with magnesium, JDS05120, and sulfate | ||||||
![]() | 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 | ![]() ![]() ![]() | ||||||
![]() | 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 | ![]() | 155.7 KB | Display | ![]() |
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PDB format | ![]() | 120.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 739 KB | Display | ![]() |
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Full document | ![]() | 742.2 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 21.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nfiC ![]() 4nfkC ![]() 4pvxC ![]() 4pvyC ![]() 4demS 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
#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 | ChemComp-JD5 / [({ | ||||
#3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.48 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 25.5% PEG MME 2000, 0.17M ammonium sulfate, 15% glycerol, 0.09M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 20, 2013 |
Radiation | Monochromator: ACCEL/BRUKER DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. all: 27177 / Num. obs: 27177 / % possible obs: 99.4 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 31.3 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 4 / Num. unique all: 1311 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4DEM Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 10.68 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.148 / 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: 46.148 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.051→2.104 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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