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Yorodumi- PDB-1lv8: Crystal structure of calf spleen purine nucleoside phosphorylase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lv8 | ||||||
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Title | Crystal structure of calf spleen purine nucleoside phosphorylase in a new space group with full trimer in the asymmetric unit | ||||||
Components | PURINE NUCLEOSIDE PHOSPHORYLASE | ||||||
Keywords | TRANSFERASE / PNP / PURIE NUCLEOSIDE PHOSPHORYLASE / PENTOSYLTRANSFERASE / NE 2 / 6-DIAMINOPURINE MULTISUBSTRATE ANALOGUE INHIBITOR | ||||||
Function / homology | Function and homology information guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine ribonucleoside salvage / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Bzowska, A. / Koellner, G. / Wielgus-Kutrowska, B. / Stroh, A. / Raszewski, G. / Holy, A. / Steiner, T. / Frank, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Crystal structure of calf spleen purine nucleoside phosphorylase with two full trimers in the asymmetric unit: important implications for the mechanism of catalysis Authors: Bzowska, A. / Koellner, G. / Wielgus-Kutrowska, B. / Stroh, A. / Raszewski, G. / Holy, A. / Steiner, T. / Frank, J. #1: Journal: NUCLEOSIDES NUCLEOTIDES NUCLEIC ACIDS / Year: 2003 Title: Crystal Structure of Calf Spleen Purine Nucleoside in a Complex with Multisubstrate Analogue Inhibitor with 2,6-Diaminopurine Aglycone Authors: Koellner, G. / Stroh, A. / Raszewski, G. / Holy, A. / Bzowska, A. #2: Journal: J.Mol.Biol. / Year: 1997 Title: Crystals Structure of Calf Spleen Purine Nucleoside Phosphorylase in a Complex with Hypoxanthine at 2.15 A Resolution Authors: Koellner, G. / Luic, M. / Shugar, D. / Saenger, W. / Bzowska, A. #3: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2001 Title: Calf Spleen Purine Nucleoside Phsophorylase: Crystal Structure of its Ternary Complex with an N(7)-Acycloguanosine Inhibitor and a Phosphate Anion Authors: Luic, M. / Koellner, G. / Shugar, D. / Saenger, W. / Bzowska, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lv8.cif.gz | 344.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lv8.ent.gz | 276.7 KB | Display | PDB format |
PDBx/mmJSON format | 1lv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lv8_validation.pdf.gz | 716.4 KB | Display | wwPDB validaton report |
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Full document | 1lv8_full_validation.pdf.gz | 776.3 KB | Display | |
Data in XML | 1lv8_validation.xml.gz | 41.1 KB | Display | |
Data in CIF | 1lv8_validation.cif.gz | 61.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/1lv8 ftp://data.pdbj.org/pub/pdb/validation_reports/lv/1lv8 | HTTPS FTP |
-Related structure data
Related structure data | 1lvuC 1fxuS 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: 32126.557 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: SPLEEN References: UniProt: P55859, purine-nucleoside phosphorylase #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-9PP / #4: 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: 49.61 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.25 Details: HEPES, PEG400, CaCl2, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9101 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9101 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→19.9 Å / Num. obs: 98387 / % possible obs: 99.7 % / Observed criterion σ(I): 15.7 / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.055 |
Reflection shell | Resolution: 2.3→2.44 Å / Num. unique all: 98387 / % possible all: 99.7 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 84155 |
Reflection shell | *PLUS % possible obs: 99.7 % / Rmerge(I) obs: 0.377 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FXU Resolution: 2.3→19.85 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber Details: PROTEIN WAS CO-CRYSTALLIZED WITH 9PP FROM 19-31% PEG-400 IN 100 MM HEPES BUFFER, PH 7.25; 100MM CACL2 PROTEIN WAS MIXED WITH 9PP AT A 1:5 (PNP TRIMER : INHIBITOR) MOLAR RATIO
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.0256 Å2 / ksol: 0.323506 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43 Å2
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Refine analyze | Luzzati coordinate error free: 0.36 Å / Luzzati sigma a free: 0.35 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / % reflection Rfree: 10.3 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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