+Open data
-Basic information
Entry | Database: PDB / ID: 1ko8 | ||||||
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Title | Crystal structure of gluconate kinase | ||||||
Components | Gluconate kinase | ||||||
Keywords | TRANSFERASE / alfa/beta | ||||||
Function / homology | Function and homology information gluconokinase / gluconokinase activity / D-gluconate catabolic process / protein homodimerization activity / ATP binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Kraft, L. / Sprenger, G.A. / Lindqvist, Y. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Conformational changes during the catalytic cycle of gluconate kinase as revealed by X-ray crystallography. Authors: Kraft, L. / Sprenger, G.A. / Lindqvist, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ko8.cif.gz | 79.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ko8.ent.gz | 60.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ko8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ko8_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1ko8_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1ko8_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 1ko8_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/1ko8 ftp://data.pdbj.org/pub/pdb/validation_reports/ko/1ko8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer |
-Components
#1: Protein | Mass: 19572.295 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: gntk / Plasmid: pJF119EH / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P46859, gluconokinase #2: Sugar | #3: Chemical | ChemComp-MG / | #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: 2.47 Å3/Da / Density % sol: 50.29 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: PEG6000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.093 Å |
Detector | Type: BRUKER SMART 1000 / Detector: CCD / Date: Jun 20, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.093 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→48.8 Å / Num. all: 14896 / Num. obs: 14896 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 51.3 Å2 / Rsym value: 0.094 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 2.4→2.53 Å / % possible all: 99.4 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 61464 / Rmerge(I) obs: 0.094 |
Reflection shell | *PLUS % possible obs: 99.4 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 1.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→25 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.884 / SU B: 14.537 / SU ML: 0.339 / Cross valid method: THROUGHOUT / ESU R: 0.508 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.127 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.348→2.409 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 2.4 Å / Rfactor obs: 0.254 / Rfactor Rfree: 0.309 / Rfactor Rwork: 0.254 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.517 / Rfactor Rwork: 0.382 / Rfactor obs: 0.382 |