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Yorodumi- PDB-2ji4: Human phosphoribosylpyrophosphate synthetase - associated protein... -
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-Basic information
Entry | Database: PDB / ID: 2ji4 | ||||||
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Title | Human phosphoribosylpyrophosphate synthetase - associated protein 41 (PAP41) | ||||||
Components | PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 2 | ||||||
Keywords | TRANSFERASE / PHOSPHORYLATION / NUCLEOTIDE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information ribose phosphate diphosphokinase complex / ribose phosphate diphosphokinase activity / nucleotide biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / nucleoside metabolic process / purine nucleotide biosynthetic process / enzyme inhibitor activity / nucleobase-containing compound metabolic process / bone development / magnesium ion binding ...ribose phosphate diphosphokinase complex / ribose phosphate diphosphokinase activity / nucleotide biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / nucleoside metabolic process / purine nucleotide biosynthetic process / enzyme inhibitor activity / nucleobase-containing compound metabolic process / bone development / magnesium ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Moche, M. / Lehtio, L. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. ...Moche, M. / Lehtio, L. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg-Schiavone, L. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Nordlund, P. | ||||||
Citation | Journal: To be Published Title: Human Phosphoribosylpyrophosphate Synthetase -Associated Protein 41 (Pap41) Authors: Moche, M. / Lehtio, L. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / ...Authors: Moche, M. / Lehtio, L. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg-Schiavone, L. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Nordlund, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ji4.cif.gz | 74.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ji4.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ji4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/2ji4 ftp://data.pdbj.org/pub/pdb/validation_reports/ji/2ji4 | HTTPS FTP |
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-Related structure data
Related structure data | 2c4kS 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: 42158.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60256 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | OUR CONSTRUCT CONTAINS 1. AN N-TERMINAL HEXAHISTID | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 48.47 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 19, 2006 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 14119 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 2.5→2.7 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 7.4 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C4K Resolution: 2.55→19.73 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.904 / SU B: 12.206 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.465 / ESU R Free: 0.308 / 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: 42.63 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→19.73 Å
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Refine LS restraints |
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