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Yorodumi- PDB-6xz2: Crystal structure of E. Coli purine nucleoside phosphorylase muta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xz2 | ||||||
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Title | Crystal structure of E. Coli purine nucleoside phosphorylase mutant Y160W with SO4 and Formycin A | ||||||
Components | Purine nucleoside phosphorylase DeoD-type | ||||||
Keywords | TRANSFERASE / trimer of dimers / single tryptophan mutant / protein-inhibitor complex | ||||||
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: 1.65000304482 Å | ||||||
Authors | Narczyk, M. / Bzowska, A. | ||||||
Citation | Journal: Sci Rep / Year: 2021 Title: Single tryptophan Y160W mutant of homooligomeric E. coli purine nucleoside phosphorylase implies that dimers forming the hexamer are functionally not equivalent. Authors: Narczyk, M. / Mioduszewski, L. / Oksiejuk, A. / Winiewska-Szajewska, M. / Wielgus-Kutrowska, B. / Gojdz, A. / Ciesla, J. / Bzowska, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xz2.cif.gz | 185.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xz2.ent.gz | 118.9 KB | Display | PDB format |
PDBx/mmJSON format | 6xz2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/6xz2 ftp://data.pdbj.org/pub/pdb/validation_reports/xz/6xz2 | HTTPS FTP |
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-Related structure data
Related structure data | 1ecpS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25744.668 Da / Num. of mol.: 3 / Mutation: Y160W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: deoD, pup, b4384, JW4347 / Production host: Escherichia coli (E. coli) References: UniProt: P0ABP8, purine-nucleoside phosphorylase #2: Chemical | #3: Chemical | ChemComp-FMC / ( | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.25 Å3/Da / Density % sol: 62.18 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 50 mM citrate buffer pH 5.2, 14 % ammonium sulphate (w/v) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.0064 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0064 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→104.3 Å / Num. obs: 123021 / % possible obs: 99.42 % / Redundancy: 99.8 % / Biso Wilson estimate: 22.4977063367 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.028 / Rrim(I) all: 0.177 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.65→1.68 Å / Rmerge(I) obs: 1.483 / Num. unique obs: 5869 / CC1/2: 0.821 / Rpim(I) all: 0.26 / Rrim(I) all: 1.507 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ecp Resolution: 1.65000304482→78.7072722459 Å / SU ML: 0.157720237261 / Cross valid method: FREE R-VALUE / σ(F): 1.35096088804 / Phase error: 18.312385071
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.1661880984 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65000304482→78.7072722459 Å
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Refine LS restraints |
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LS refinement shell |
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