+Open data
-Basic information
Entry | Database: PDB / ID: 3ry7 | ||||||
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Title | Crystal Structure of Sa239 | ||||||
Components | Ribokinase | ||||||
Keywords | TRANSFERASE / Sa239 / Staphylococcus aureus / Ribokinase | ||||||
Function / homology | Function and homology information ribokinase / ribokinase activity / D-ribose catabolic process / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Li, J. / Wu, M. / Wang, L. / Zang, J. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2012 Title: Crystal structure of Sa239 reveals the structural basis for the activation of ribokinase by monovalent cations. Authors: Li, J. / Wang, C. / Wu, Y. / Wu, M. / Wang, L. / Wang, Y. / Zang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ry7.cif.gz | 75.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ry7.ent.gz | 56.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ry7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/3ry7 ftp://data.pdbj.org/pub/pdb/validation_reports/ry/3ry7 | HTTPS FTP |
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-Related structure data
Related structure data | 1gqtS S: Starting model for refinement |
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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: 32475.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: COL / Gene: rbsK, SACOL0253 / Production host: Escherichia coli (E. coli) References: UniProt: Q5HJA8, UniProt: A0A0H2WZY4*PLUS, ribokinase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.9 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 23% PEG 3000 (w/v), 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å |
Detector | Type: RAYONIX MX-325 / Detector: CCD / Date: Sep 12, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. all: 24295 / Num. obs: 24271 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.1 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.093 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.15→2.19 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GQT Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.93 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.339 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.146→2.202 Å / Total num. of bins used: 20
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