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Yorodumi- PDB-4b8s: Crystal Structure of Thermococcus litoralis ADP-dependent Glucoki... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b8s | ||||||
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Title | Crystal Structure of Thermococcus litoralis ADP-dependent Glucokinase (GK) | ||||||
Components | ADP-DEPENDENT GLUCOKINASE | ||||||
Keywords | TRANSFERASE / RIBOKINASE SUPERFAMILY | ||||||
Function / homology | Function and homology information ADP-specific glucose/glucosamine kinase / ADP-specific glucokinase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / glucokinase activity / glycolytic process / glucose metabolic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | THERMOCOCCUS LITORALIS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å | ||||||
Authors | Herrera-Morande, A. / Rivas-Pardo, J.A. / Fernandez, F.J. / Guixe, V. / Vega, M.C. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Crystal Structure, Saxs and Kinetic Mechanism of Hyperthermophilic Adp-Dependent Glucokinase from Thermococcus Litoralis Reveal a Conserved Mechanism for Catalysis. Authors: Rivas-Pardo, J.A. / Herrera-Morande, A. / Castro-Fernandez, V. / Fernandez, F.J. / Vega, M.C. / Guixe, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b8s.cif.gz | 208 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b8s.ent.gz | 167.1 KB | Display | PDB format |
PDBx/mmJSON format | 4b8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b8s_validation.pdf.gz | 755.4 KB | Display | wwPDB validaton report |
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Full document | 4b8s_full_validation.pdf.gz | 760 KB | Display | |
Data in XML | 4b8s_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 4b8s_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/4b8s ftp://data.pdbj.org/pub/pdb/validation_reports/b8/4b8s | HTTPS FTP |
-Related structure data
Related structure data | 4b8rC 1gc5S C: citing same article (ref.) 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: 53688.184 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOCOCCUS LITORALIS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS References: UniProt: Q7M537, ADP-specific glucose/glucosamine kinase | ||||
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#2: Sugar | ChemComp-GLC / | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-AMP / | #5: 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: 3.98 Å3/Da / Density % sol: 69.09 % / Description: NONE |
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Crystal grow | pH: 5.2 Details: 1.5 M SODIUM CITRATE PH 5.2, 5 MM DTT, 6 MM MG-ADPBETAS AND 30 MM D-GLC. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9794 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→35 Å / Num. obs: 33911 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 47.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.58→2.65 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3.5 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GC5 Resolution: 2.58→34.85 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.927 / SU B: 15 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
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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: 50.637 Å2
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Refinement step | Cycle: LAST / Resolution: 2.58→34.85 Å
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Refine LS restraints |
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