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Yorodumi- PDB-3txv: Crystal structure of a probable tagatose 6 phosphate kinase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3txv | ||||||
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Title | Crystal structure of a probable tagatose 6 phosphate kinase from Sinorhizobium meliloti 1021 | ||||||
Components | Probable tagatose 6-phosphate kinase | ||||||
Keywords | TRANSFERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC | ||||||
Function / homology | Function and homology information tagatose-6-phosphate kinase / tagatose-6-phosphate kinase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Sinorhizobium meliloti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 probable tagatose 6 phosphate kinase from Sinorhizobium meliloti 1021 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 | 3txv.cif.gz | 85.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3txv.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 3txv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3txv_validation.pdf.gz | 429.8 KB | Display | wwPDB validaton report |
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Full document | 3txv_full_validation.pdf.gz | 435.9 KB | Display | |
Data in XML | 3txv_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 3txv_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/3txv ftp://data.pdbj.org/pub/pdb/validation_reports/tx/3txv | HTTPS FTP |
-Related structure data
Related structure data | 2fiqS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 49421.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: RB0951, SM_b21373 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q92UY3, tagatose-6-phosphate kinase |
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#2: 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: 2.79 Å3/Da / Density % sol: 55.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M CaCl2, 0.1M Hepes pH 7.5, 28% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 2011 / Details: mirrors |
Radiation | Monochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 14349 / Num. obs: 14349 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 35 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 34.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 4 / Num. unique all: 1387 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FIQ Resolution: 2.8→48.68 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.866 / SU B: 15.176 / SU ML: 0.305 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.823 / ESU R Free: 0.386 / 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: 44.606 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→48.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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