+Open data
-Basic information
Entry | Database: PDB / ID: 2ai3 | ||||||
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Title | Purine nucleoside phosphorylase from calf spleen | ||||||
Components | Purine nucleoside phosphorylase | ||||||
Keywords | TRANSFERASE / purine nucleoside phosphorylase / multisubstrate analog 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: 1.7 Å | ||||||
Authors | Toms, A.V. / Wang, W. / Li, Y. / Ganem, B. / Ealick, S.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Novel multisubstrate inhibitors of mammalian purine nucleoside phosphorylase. Authors: Toms, A.V. / Wang, W. / Li, Y. / Ganem, B. / Ealick, S.E. #1: Journal: Biochemistry / Year: 1998 Title: Calf Spleen Purine Nucleoside Phosphorylase Complexed with Substrates and Substrate Analogs. Authors: Mao, C. / Cook, W.J. / Zhou, M. / Fedorov, A.A. / Almo, S.C. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ai3.cif.gz | 74.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ai3.ent.gz | 53.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ai3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/2ai3 ftp://data.pdbj.org/pub/pdb/validation_reports/ai/2ai3 | HTTPS FTP |
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-Related structure data
Related structure data | 2ai1C 2ai2C 1a9pS C: citing same article (ref.) 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 on special symmetry positions |
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Details | The biological assembly is a trimer generated from the monomer in the asymmetric unit. |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 32127.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: calf spleen purine nucleoside phosphorylase purchased from Sigma Co. Source: (natural) Bos taurus (cattle) / Organ: spleen References: UniProt: P55859, purine-nucleoside phosphorylase |
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-Non-polymers , 5 types, 179 molecules
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-144 / |
#5: Chemical | ChemComp-P2G / ( |
#6: 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: 2.1 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PEG2K MME , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.928 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 28, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.928 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. all: 30699 / Num. obs: 29787 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.7 % / Biso Wilson estimate: 24.8 Å2 / Rsym value: 0.046 / Net I/σ(I): 42 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 6 % / Mean I/σ(I) obs: 5 / Num. unique all: 2969 / Rsym value: 0.448 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1A9P Resolution: 1.7→31.33 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 515560.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.1855 Å2 / ksol: 0.349564 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→31.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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