+Open data
-Basic information
Entry | Database: PDB / ID: 6znx | ||||||
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Title | Ribokinase from Thermus Species | ||||||
Components | Ribokinase | ||||||
Keywords | TRANSFERASE / ADP | ||||||
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. 2.9 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Timofeev, V.I. / Abramchik, Y.A. / Tuzova, E.S. / Esipova, L.V. / Mikheeva, O.O. / Kostromina, M.A. / Kuranova, I.P. / Esipov, R.S. | ||||||
Citation | Journal: To Be Published Title: Ribokinase from Thermus Species Authors: Timofeev, V.I. / Abramchik, Y.A. / Tuzova, E.S. / Esipova, L.V. / Mikheeva, O.O. / Kostromina, M.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 | 6znx.cif.gz | 220.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6znx.ent.gz | 177.1 KB | Display | PDB format |
PDBx/mmJSON format | 6znx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6znx_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6znx_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6znx_validation.xml.gz | 45.1 KB | Display | |
Data in CIF | 6znx_validation.cif.gz | 62.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/6znx ftp://data.pdbj.org/pub/pdb/validation_reports/zn/6znx | HTTPS FTP |
-Related structure data
Related structure data | 4xdaS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31026.439 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus sp. 2.9 (bacteria) / Gene: rbsK, QT17_05185 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B0SD75, ribokinase #2: Chemical | ChemComp-ADP / #3: 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: 2.28 Å3/Da / Density % sol: 45.99 % |
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Crystal grow | Temperature: 293 K / Method: counter-diffusion / Details: PEG |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 41928 / % possible obs: 96.91 % / Redundancy: 3.18 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 5.2958 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.28 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 4.47 / Num. unique obs: 6150 / % possible all: 97.73 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XDA Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.882 / SU B: 9.44 / SU ML: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.697 / ESU R Free: 0.31 / 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: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.21 Å2 / Biso mean: 36.213 Å2 / Biso min: 3.4 Å2
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Refinement step | Cycle: final / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.461 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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