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Yorodumi- PDB-4nfi: Crystal structure of human FPPS in complex with magnesium and JDS05120 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nfi | ||||||
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Title | Crystal structure of human FPPS in complex with magnesium and JDS05120 | ||||||
Components | Farnesyl pyrophosphate synthaseDimethylallyltranstransferase | ||||||
Keywords | Transferase/Transferase inhibitor / Transferase-Transferase inhibitor complex | ||||||
Function / homology | Function and homology information 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å | ||||||
Authors | Park, J. / De Schutter, J.W. / Tsantrizos, Y.S. / Berghuis, A.M. | ||||||
Citation | Journal: PLoS ONE / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nfi.cif.gz | 161.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nfi.ent.gz | 125.7 KB | Display | PDB format |
PDBx/mmJSON format | 4nfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/4nfi ftp://data.pdbj.org/pub/pdb/validation_reports/nf/4nfi | HTTPS FTP |
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-Related structure data
Related structure data | 4nfjC 4nfkC 4pvxC 4pvyC 4demS C: citing same article (ref.) S: Starting model for refinement |
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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: 43144.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS, FPS, KIAA1293 / Production host: Escherichia coli (E. coli) References: UniProt: P14324, (2E,6E)-farnesyl diphosphate synthase, dimethylallyltranstransferase | ||
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#2: Chemical | ChemComp-JD5 / [({ | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.09 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 20% PEG 3350, 0.2M magnesium formate, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
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: 1.85→50.85 Å / Num. all: 35614 / Num. obs: 35614 / % possible obs: 99.1 % / Redundancy: 9.6 % / Biso Wilson estimate: 24.99 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 29.54 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 4.98 / Num. unique all: 2598 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 4DEM Resolution: 1.85→50.85 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.216 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.111 / 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: 37.23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→50.85 Å
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Refine LS restraints |
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