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Yorodumi- PDB-3t69: Crystal structure of a putative 2-dehydro-3-deoxygalactonokinase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t69 | ||||||
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Title | Crystal structure of a putative 2-dehydro-3-deoxygalactonokinase protein from Sinorhizobium meliloti | ||||||
Components | Putative 2-dehydro-3-deoxygalactonokinase | ||||||
Keywords | TRANSFERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / 2-dehydro-3-deoxygalactonokinase | ||||||
Function / homology | Function and homology information 2-dehydro-3-deoxygalactonokinase / 2-dehydro-3-deoxygalactonokinase activity / D-galactonate catabolic process / ATP binding Similarity search - Function | ||||||
Biological species | Sinorhizobium meliloti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å | ||||||
Authors | Agarwal, R. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Agarwal, R. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a putative 2-dehydro-3-deoxygalactonokinase protein from Sinorhizobium meliloti Authors: Agarwal, R. / Almo, S.C. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t69.cif.gz | 122 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t69.ent.gz | 95.2 KB | Display | PDB format |
PDBx/mmJSON format | 3t69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/3t69 ftp://data.pdbj.org/pub/pdb/validation_reports/t6/3t69 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34822.238 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: dgoK1, R00825, SMc00881 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL References: UniProt: Q92RN7, 2-dehydro-3-deoxygalactonokinase #2: Chemical | ChemComp-SO4 / #3: 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: 2.98 Å3/Da / Density % sol: 58.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M BIS-TRIS pH5.5, 2M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9783 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 28, 2011 / Details: mirrors |
Radiation | Monochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9783 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. all: 27367 / Num. obs: 27367 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 12.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.55→43.46 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.901 / SU B: 10.082 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.429 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.275 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→43.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.545→2.611 Å / Total num. of bins used: 20
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