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Yorodumi- PDB-4h5e: Crystal structure of human FPPS in ternary complex with YS0470 an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h5e | ||||||
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Title | Crystal structure of human FPPS in ternary complex with YS0470 and isopentenyl pyrophosphate | ||||||
Components | Farnesyl pyrophosphate synthase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Transferase / 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 / FOURIER SYNTHESIS / Resolution: 2.04 Å | ||||||
Authors | Park, J. / Lin, Y.-S. / Tsantrizos, Y.S. / Berghuis, A.M. | ||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2012 Title: Ternary complex structures of human farnesyl pyrophosphate synthase bound with a novel inhibitor and secondary ligands provide insights into the molecular details of the enzyme's active site closure. Authors: Park, J. / Lin, Y.S. / De Schutter, J.W. / 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 | 4h5e.cif.gz | 158.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h5e.ent.gz | 123 KB | Display | PDB format |
PDBx/mmJSON format | 4h5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/4h5e ftp://data.pdbj.org/pub/pdb/validation_reports/h5/4h5e | HTTPS FTP |
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-Related structure data
Related structure data | 4h5cC 4h5dC 4demS 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: 43144.980 Da / Num. of mol.: 1 / Fragment: UNP residues 67-419 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Genus: human / Gene: FDPS, FPS, KIAA1293 / Production host: Escherichia coli (E. coli) References: UniProt: P14324, dimethylallyltranstransferase, (2E,6E)-farnesyl diphosphate synthase | ||
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#2: Chemical | ChemComp-YS4 / [({ | ||
#3: Chemical | ChemComp-IPR / | ||
#4: Chemical | #5: 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: 2.35 Å3/Da / Density % sol: 47.73 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 30% PEG 300, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 17, 2011 |
Radiation | Monochromator: Confocal blue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→50 Å / Num. all: 26486 / Num. obs: 26486 / % possible obs: 100 % / Redundancy: 27.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 47.7 |
Reflection shell | Resolution: 2.04→2.09 Å / Redundancy: 26.2 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 6.9 / Num. unique all: 1289 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4DEM Resolution: 2.04→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.05 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 44.763 Å2
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Refinement step | Cycle: LAST / Resolution: 2.04→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.044→2.097 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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