+Open data
-Basic information
Entry | Database: PDB / ID: 7eym | ||||||
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Title | Crystal structure of Vibrio cholerae ppnP | ||||||
Components | Pyrimidine/purine nucleoside phosphorylase | ||||||
Keywords | HYDROLASE / Pyrimidine / purine / nucleoside phosphorylase | ||||||
Function / homology | Function and homology information guanosine phosphorylase / pyrimidine-nucleoside phosphorylase / thymidine phosphorylase / pyrimidine-nucleoside phosphorylase activity / thymidine phosphorylase activity / uridine phosphorylase / uridine phosphorylase activity / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 | 7eym.cif.gz | 52.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eym.ent.gz | 35.9 KB | Display | PDB format |
PDBx/mmJSON format | 7eym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/7eym ftp://data.pdbj.org/pub/pdb/validation_reports/ey/7eym | HTTPS FTP |
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-Related structure data
Related structure data | 7eyjSC 7eykC 7eylC 7eypC 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: 10273.443 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: ppnP / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H6V0E6 #2: 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: 2.08 Å3/Da / Density % sol: 40.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium sulfate, 30% w/v Polyethylene glycol 8,000 |
-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: 35454 / % possible obs: 99.6 % / Redundancy: 12.5 % / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.032 / Rrim(I) all: 0.117 / Net I/σ(I): 26.333 |
Reflection shell | Resolution: 1.38→1.43 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.901 / Mean I/σ(I) obs: 1.667 / Num. unique obs: 6596 / CC1/2: 0.576 / CC star: 0.855 / Rpim(I) all: 0.364 / Rrim(I) all: 0.976 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7EYJ 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: 17.44 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.38→20 Å
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Refine LS restraints |
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