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Yorodumi- PDB-4tta: Crystal structure of double mutant E. Coli purine nucleoside phos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tta | ||||||
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Title | Crystal structure of double mutant E. Coli purine nucleoside phosphorylase with 2 FMC molecules | ||||||
Components | Purine nucleoside phosphorylase DeoD-type | ||||||
Keywords | TRANSFERASE / formicyn A | ||||||
Function / homology | Function and homology information purine nucleoside interconversion / guanosine phosphorylase activity / purine nucleoside catabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / DNA damage response / membrane / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Stefanic, Z. / Bzowska, A. | ||||||
Citation | Journal: Sci Rep / Year: 2018 Title: Crystallographic snapshots of ligand binding to hexameric purine nucleoside phosphorylase and kinetic studies give insight into the mechanism of catalysis. Authors: Stefanic, Z. / Narczyk, M. / Mikleusevic, G. / Kazazic, S. / Bzowska, A. / Luic, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tta.cif.gz | 305.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tta.ent.gz | 244.6 KB | Display | PDB format |
PDBx/mmJSON format | 4tta.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/4tta ftp://data.pdbj.org/pub/pdb/validation_reports/tt/4tta | HTTPS FTP |
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-Related structure data
Related structure data | 4ts3C 4ts9C 4ttiC 4ttjC 1k9sS 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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Details | The biological assembly is a hexamer. One hexamer is found in asymmetric unit. |
-Components
#1: Protein | Mass: 25591.508 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) References: UniProt: U0SVH6, UniProt: P0ABP8*PLUS, purine-nucleoside phosphorylase #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: 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: 2.4 Å3/Da / Density % sol: 48.1 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: 50 mM citric buffer, 32 % ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97977 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97977 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.99→48 Å / Num. obs: 100218 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 12.8 % / Biso Wilson estimate: 21.695 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.142 / Rrim(I) all: 0.148 / Net I/σ(I): 16.49 / Num. measured all: 1280788 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1k9s Resolution: 2→48 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.68 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.22 Å2 / Biso mean: 16.7794 Å2 / Biso min: 2.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→48 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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