+Open data
-Basic information
Entry | Database: PDB / ID: 2j4e | ||||||
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Title | THE ITP COMPLEX OF HUMAN INOSINE TRIPHOSPHATASE | ||||||
Components | INOSINE TRIPHOSPHATE PYROPHOSPHATASE | ||||||
Keywords | HYDROLASE / NUCLEOTIDE METABOLISM / ITP / IMP / DISEASE MUTATION / INOSINE TRIPHOSPHATE PYROPHOSPHOHYDROLASE / INOSINE TRIPHOSPHATASE DEFICIENCY | ||||||
Function / homology | Function and homology information ITP catabolic process / deoxyribonucleoside triphosphate catabolic process / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleoside triphosphate catabolic process / nucleotide diphosphatase / nucleoside triphosphate diphosphatase activity / Ribavirin ADME / Purine catabolism ...ITP catabolic process / deoxyribonucleoside triphosphate catabolic process / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleoside triphosphate catabolic process / nucleotide diphosphatase / nucleoside triphosphate diphosphatase activity / Ribavirin ADME / Purine catabolism / chromosome organization / intracellular membrane-bounded organelle / nucleotide binding / nucleoplasm / identical protein binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Stenmark, P. / Kursula, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. ...Stenmark, P. / Kursula, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmbergschiavone, L. / Hogbom, M. / Kotenyova, T. / Landry, R. / Loppnau, P. / Magnusdottir, A. / Nilsson-Ehle, P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Sundstrom, M. / Uppenberg, J. / Thorsell, A.G. / Schuler, H. / Van Den Berg, S. / Wallden, K. / Weigelt, J. / Nordlund, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Crystal Structure of Human Inosine Triphosphatase: Substrate Binding and Implication of the Inosine Triphosphatase Deficiency Mutation P32T. Authors: Stenmark, P. / Kursula, P. / Flodin, S. / Graslund, S. / Landry, R. / Nordlund, P. / Schuler, H. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j4e.cif.gz | 306.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j4e.ent.gz | 250.5 KB | Display | PDB format |
PDBx/mmJSON format | 2j4e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j4e_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 2j4e_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 2j4e_validation.xml.gz | 57.5 KB | Display | |
Data in CIF | 2j4e_validation.cif.gz | 75 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/2j4e ftp://data.pdbj.org/pub/pdb/validation_reports/j4/2j4e | HTTPS FTP |
-Related structure data
Related structure data | 2carSC 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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Unit cell |
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 21612.756 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9BY32, nucleoside-triphosphate diphosphatase |
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-Non-polymers , 5 types, 184 molecules
#2: Chemical | ChemComp-ITT / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-POP / | #5: Chemical | ChemComp-IMP / | #6: 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: 3.01 Å3/Da / Density % sol: 58.81 % |
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Crystal grow | Details: 0.2 M POTASSIUM CHLORIDE, 31 % (W/V) PEG 3350, AND THE PROTEIN WAS ADDED FROM A 50 MG/ML STOCK SOLUTION CONTAINING 10MM ITP AND 20 MM HEPES PH 7.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9781 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9781 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 45773 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.8 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CAR Resolution: 2.8→19.81 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.855 / SU B: 30.579 / SU ML: 0.306 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.394 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.25 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→19.81 Å
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