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Yorodumi- PDB-4r31: Crystal structure of a putative uridine phosphorylase from Actino... -
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-Basic information
Entry | Database: PDB / ID: 4r31 | ||||||
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Title | Crystal structure of a putative uridine phosphorylase from Actinobacillus succinogenes 130Z (Target NYSGRC-029667 ) | ||||||
Components | Uridine phosphorylase | ||||||
Keywords | TRANSFERASE / phosphorylase / uridine / Structural genomics / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium | ||||||
Function / homology | Function and homology information uridine phosphorylase / nucleotide catabolic process / UMP salvage / nucleoside metabolic process / uridine phosphorylase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Actinobacillus succinogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Sampathkumar, P. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: to be published Title: Crystal structure of a putative uridine phosphorylase from Actinobacillus succinogenes 130Z (Target NYSGRC-029667 ) Authors: Sampathkumar, P. / Ahmed, M. / Attonito, J. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Himmel, D.M. / Hillerich, B. / Khafizov, K. / ...Authors: Sampathkumar, P. / Ahmed, M. / Attonito, J. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Himmel, D.M. / Hillerich, B. / Khafizov, K. / Lafleur, J. / Love, J.D. / Stead, M. / Seidel, R. / Toro, R. / Morisco, L.L. / Sojitra, S.S. / Wasserman, S.R. / Schramm, V.L. / Almo, S.C. / New York Structural Genomics Research Consortium | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r31.cif.gz | 308.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r31.ent.gz | 260.8 KB | Display | PDB format |
PDBx/mmJSON format | 4r31.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r31_validation.pdf.gz | 497.3 KB | Display | wwPDB validaton report |
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Full document | 4r31_full_validation.pdf.gz | 503.3 KB | Display | |
Data in XML | 4r31_validation.xml.gz | 60.7 KB | Display | |
Data in CIF | 4r31_validation.cif.gz | 85.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/4r31 ftp://data.pdbj.org/pub/pdb/validation_reports/r3/4r31 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30426.283 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinobacillus succinogenes (bacteria) / Strain: 130Z / Gene: Asuc_0427 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon-PlusRIL / References: UniProt: A6VLF7, uridine phosphorylase #2: Chemical | ChemComp-GOL / #3: 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: 2.52 Å3/Da / Density % sol: 51.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: Protein (20mM HEPES pH7.5, 150mM NaCl, 5% glycerol, and 5mM DTT); Reservoir (MCSG1 #81: 0.2 M sodium formate, 20% (w/v) PEG 3350); Cryoprotection (33% glycerol), Vapor Diffusion, Sitting Drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 3, 2013 / Details: MIRRORS |
Radiation | Monochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 126139 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 13.18 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 1.23 / Num. unique all: 6175 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.986 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.46 Å2 / Biso mean: 33.385 Å2 / Biso min: 13.61 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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