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Yorodumi- PDB-4e69: Crystal structure of a sugar kinase (target EFI-502132) from Ocea... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4.0E+69 | ||||||
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Title | Crystal structure of a sugar kinase (target EFI-502132) from Oceanicola granulosus, unliganded structure | ||||||
Components | 2-dehydro-3-deoxygluconokinase | ||||||
Keywords | TRANSFERASE / putative sugar kinase / enzyme function initiative / EFI / Structural Genomics | ||||||
Function / homology | Function and homology information organic substance metabolic process / kinase activity / phosphorylation / nucleotide binding Similarity search - Function | ||||||
Biological species | Oceanicola granulosus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a sugar kinase (target EFI-502132) from Oceanicola granulosus, unliganded structure Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e69.cif.gz | 264.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e69.ent.gz | 213 KB | Display | PDB format |
PDBx/mmJSON format | 4e69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/4e69 ftp://data.pdbj.org/pub/pdb/validation_reports/e6/4e69 | HTTPS FTP |
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-Related structure data
Related structure data | 3lhxS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34612.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oceanicola granulosus (bacteria) / Strain: HTCC2516 / Gene: OG2516_05533 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2CIP5 #2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | #5: 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: 2.36 Å3/Da / Density % sol: 47.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 Details: Protein (10 mM HEPES pH 7.5, 150 mM NaCl, 10% glycerol, 1 mM DTT; Reservoir (1 M LiCl, 0.1 M NaCitrate pH 4, 20% Peg 6000); Cryoprotection (Reservoir, + 20% Ethyelene Glycol), VAPOR ...Details: Protein (10 mM HEPES pH 7.5, 150 mM NaCl, 10% glycerol, 1 mM DTT; Reservoir (1 M LiCl, 0.1 M NaCitrate pH 4, 20% Peg 6000); Cryoprotection (Reservoir, + 20% Ethyelene Glycol), VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Feb 19, 2012 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. all: 84535 / Num. obs: 84535 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 19.51 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 1.6 / Num. unique all: 12335 / Rsym value: 0.837 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LHX Resolution: 1.6→28.024 Å / Occupancy max: 1 / Occupancy min: 0.26 / FOM work R set: 0.8819 / SU ML: 0.22 / σ(F): 0 / σ(I): 0 / Phase error: 19.24 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.886 Å2 / ksol: 0.361 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.74 Å2 / Biso mean: 25.4174 Å2 / Biso min: 8.49 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→28.024 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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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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