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Yorodumi- PDB-7eyk: Crystal structure of Escherichia coli ppnP-Selenomethionine derived -
+Open data
-Basic information
Entry | Database: PDB / ID: 7eyk | ||||||
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Title | Crystal structure of Escherichia coli ppnP-Selenomethionine derived | ||||||
Components | Pyrimidine/purine nucleoside phosphorylase | ||||||
Keywords | HYDROLASE / Pyrimidine / purine / nucleoside phosphorylase | ||||||
Function / homology | Function and homology information pyrimidine-nucleoside phosphorylase / pyrimidine-nucleoside phosphorylase activity / thymidine phosphorylase activity / guanosine phosphorylase activity / uridine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.38 Å | ||||||
Authors | Wen, Y. / Wu, B.X. | ||||||
Citation | Journal: Proteins / Year: 2022 Title: Crystal structures of a new class of pyrimidine/purine nucleoside phosphorylase revealed a Cupin fold. Authors: Wen, Y. / Li, X. / Guo, W. / Wu, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7eyk.cif.gz | 32.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eyk.ent.gz | 22.7 KB | Display | PDB format |
PDBx/mmJSON format | 7eyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7eyk_validation.pdf.gz | 406 KB | Display | wwPDB validaton report |
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Full document | 7eyk_full_validation.pdf.gz | 405.9 KB | Display | |
Data in XML | 7eyk_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 7eyk_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/7eyk ftp://data.pdbj.org/pub/pdb/validation_reports/ey/7eyk | HTTPS FTP |
-Related 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: 10468.095 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: ppnP / Production host: Escherichia coli (E. coli) / References: UniProt: P0C037 |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.26 M Ammonium sulfate (dibasic), 0.1M Sodium cacodylate/Hydrochloric acid pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→50 Å / Num. obs: 21812 / % possible obs: 100 % / Redundancy: 19.8 % / CC1/2: 0.96 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.018 / Rrim(I) all: 0.079 / Net I/σ(I): 36.41 |
Reflection shell | Resolution: 1.38→1.43 Å / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 7 / Num. unique obs: 2162 / CC1/2: 0.959 / CC star: 0.989 / Rpim(I) all: 0.116 / Rrim(I) all: 0.518 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.38→20 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 16.32 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.38→20 Å
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Refine LS restraints |
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