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Yorodumi- PDB-4bc5: Crystal structure of human D-xylulokinase in complex with inhibit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bc5 | ||||||
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Title | Crystal structure of human D-xylulokinase in complex with inhibitor 5- deoxy-5-fluoro-D-xylulose | ||||||
Components | XYLULOSE KINASE | ||||||
Keywords | TRANSFERASE / GLUCURONATE XYLULOKINASE PATHWAY / FGGY CARBOHYDRATE KINASE / INHIBITOR | ||||||
Function / homology | Function and homology information xylulose metabolic process / D-xylulokinase activity / xylulokinase / xylulose catabolic process / D-glucuronate catabolic process to D-xylulose 5-phosphate / Formation of xylulose-5-phosphate / D-xylose metabolic process / generation of precursor metabolites and energy / carbohydrate metabolic process / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Bunker, R.D. / Loomes, K.M. / Baker, E.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structure and Function of Human Xylulokinase, an Enzyme with Important Roles in Carbohydrate Metabolism Authors: Bunker, R.D. / Bulloch, E.M.M. / Dickson, J.M.J. / Loomes, K.M. / Baker, E.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bc5.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4bc5.ent.gz | 959 KB | Display | PDB format |
PDBx/mmJSON format | 4bc5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bc5_validation.pdf.gz | 467.4 KB | Display | wwPDB validaton report |
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Full document | 4bc5_full_validation.pdf.gz | 479.5 KB | Display | |
Data in XML | 4bc5_validation.xml.gz | 59.6 KB | Display | |
Data in CIF | 4bc5_validation.cif.gz | 85.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/4bc5 ftp://data.pdbj.org/pub/pdb/validation_reports/bc/4bc5 | HTTPS FTP |
-Related structure data
Related structure data | 4bc2C 4bc3C 4bc4C 4b6t 4b6y C: citing same article (ref.) |
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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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 58566.047 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPROEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75191, xylulokinase #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: 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: 2.8 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | Details: 200 MM MES/KOH PH 5.9, 13% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→33.96 Å / Num. obs: 129196 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 39.78 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.98→2.01 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.45 / Mean I/σ(I) obs: 0.7 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HUMAN D-XYLULOKINASE DETERMINED BY TWO- ENERGY SELENIUM MAD Resolution: 1.98→28.98 Å / Cor.coef. Fo:Fc: 0.9557 / Cor.coef. Fo:Fc free: 0.9493 / SU R Cruickshank DPI: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.133 / SU Rfree Blow DPI: 0.117 / SU Rfree Cruickshank DPI: 0.12
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Displacement parameters | Biso mean: 48.77 Å2
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Refine analyze | Luzzati coordinate error obs: 0.269 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→28.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.03 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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