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Yorodumi- PDB-3efh: Crystal structure of human phosphoribosyl pyrophosphate synthetase 1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3efh | ||||||
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Title | Crystal structure of human phosphoribosyl pyrophosphate synthetase 1 | ||||||
Components | Ribose-phosphate pyrophosphokinase 1 | ||||||
Keywords | TRANSFERASE / Charcot-Marie-Tooth disease / Deafness / Disease mutation / Gout / Kinase / Magnesium / Metal-binding / Nucleotide biosynthesis / Polymorphism | ||||||
Function / homology | Function and homology information 5-Phosphoribose 1-diphosphate biosynthesis / hypoxanthine biosynthetic process / ribose phosphate diphosphokinase complex / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / ribonucleoside monophosphate biosynthetic process / urate biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / pyrimidine nucleotide biosynthetic process / purine nucleotide biosynthetic process ...5-Phosphoribose 1-diphosphate biosynthesis / hypoxanthine biosynthetic process / ribose phosphate diphosphokinase complex / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / ribonucleoside monophosphate biosynthetic process / urate biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / pyrimidine nucleotide biosynthetic process / purine nucleotide biosynthetic process / purine nucleobase metabolic process / kinase activity / nervous system development / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Li, X. / Peng, X. / Li, Y. | ||||||
Citation | Journal: To be Published Title: Crystal structure of human phosphoribosyl pyrophosphate synthetase 1 Authors: Peng, X. / Li, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3efh.cif.gz | 126.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3efh.ent.gz | 98.1 KB | Display | PDB format |
PDBx/mmJSON format | 3efh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3efh_validation.pdf.gz | 448 KB | Display | wwPDB validaton report |
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Full document | 3efh_full_validation.pdf.gz | 459.7 KB | Display | |
Data in XML | 3efh_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 3efh_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/3efh ftp://data.pdbj.org/pub/pdb/validation_reports/ef/3efh | HTTPS FTP |
-Related structure data
Related structure data | 2hcrS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 35950.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRPS1 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P60891, ribose-phosphate diphosphokinase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.62 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.3 Details: 2.1M ammonium sulfate, 0.1M sodium acetate, 10% (v/v) glycerol, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 18, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→42.295 Å / Num. all: 18873 / Num. obs: 18518 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.4 % / Biso Wilson estimate: 50.4 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2623 / Rsym value: 0.345 / % possible all: 88.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HCR Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.566 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.328 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.116 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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