+Open data
-Basic information
Entry | Database: PDB / ID: 8cqx | ||||||
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Title | Ribokinase from T.sp mutant A92G | ||||||
Components | Ribokinase | ||||||
Keywords | HYDROLASE / mutant / 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 | Thermus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Timofeev, V.I. / Shevtsov, M.B. / Abramchik, Y.A. / Kostromina, M.A. / Zayats, E.A. / Kuranova, I.P. / Esipov, R.S. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Ribokinase from T.sp mutant A92G Authors: Timofeev, V.I. / Shevtsov, M.B. / Abramchik, Y.A. / Kostromina, M.A. / Zayats, E.A. / Kuranova, I.P. / Esipov, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cqx.cif.gz | 227.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cqx.ent.gz | 186.2 KB | Display | PDB format |
PDBx/mmJSON format | 8cqx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/8cqx ftp://data.pdbj.org/pub/pdb/validation_reports/cq/8cqx | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31012.416 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus sp. (bacteria) / Gene: rbsK / Production host: Thermus sp. (bacteria) / References: UniProt: A0A0B0SD75 #2: Chemical | ChemComp-ADP / #3: Chemical | #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: 2.29 Å3/Da / Density % sol: 46.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% peg3350, 0,45 M NaCl, 0,1 M citric acid pH 5.0, 5 mM MgCl2, 5 mM ADP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å |
Detector | Type: DECTRIS EIGER R 1M / Detector: PIXEL / Date: Sep 3, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→30 Å / Num. obs: 51152 / % possible obs: 99.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.133 / Rrim(I) all: 0.158 / Net I/σ(I): 3.886 |
Reflection shell | Resolution: 2.27→2.39 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 25537 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→29.52 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.844 / SU B: 10.246 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.454 / ESU R Free: 0.311 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.734 Å2
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Refinement step | Cycle: 1 / Resolution: 2.27→29.52 Å
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