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Yorodumi- PDB-1kew: The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kew | ||||||
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Title | The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar Typhimurium with thymidine diphosphate bound | ||||||
Components | dTDP-D-glucose 4,6-dehydratase | ||||||
Keywords | LYASE / Rossmann fold | ||||||
Function / homology | Function and homology information dTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase activity / O antigen biosynthetic process / dTDP-rhamnose biosynthetic process / NADH binding / lipopolysaccharide biosynthetic process / extracellular polysaccharide biosynthetic process Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Allard, S.T.M. / Beis, K. / Giraud, M.-F. / Hegeman, A.D. / Gross, J.W. / Whitfield, C. / Graninger, M. / Messner, P. / Allen, A.G. / Naismith, J.H. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Toward a structural understanding of the dehydratase mechanism. Authors: Allard, S.T. / Beis, K. / Giraud, M.F. / Hegeman, A.D. / Gross, J.W. / Wilmouth, R.C. / Whitfield, C. / Graninger, M. / Messner, P. / Allen, A.G. / Maskell, D.J. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kew.cif.gz | 173.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kew.ent.gz | 137.1 KB | Display | PDB format |
PDBx/mmJSON format | 1kew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kew_validation.pdf.gz | 651.9 KB | Display | wwPDB validaton report |
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Full document | 1kew_full_validation.pdf.gz | 665.5 KB | Display | |
Data in XML | 1kew_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 1kew_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/1kew ftp://data.pdbj.org/pub/pdb/validation_reports/ke/1kew | HTTPS FTP |
-Related structure data
Related structure data | 1kepC 1kerC 1ketC 1keuC 1g1aS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40767.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Species: Salmonella enterica / Strain: subsp. enterica serovar Typhimurium / Gene: rmlB / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P26391, dTDP-glucose 4,6-dehydratase #2: Chemical | #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: 4.74 Å3/Da / Density % sol: 74.06 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.32 Details: 0.1M MES pH 6.32, 1.5M lithium sulphate, VAPOR DIFFUSION, HANGING DROP at 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.3 | ||||||||||||||||||||||||||||||||||||||||||
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: SRS / Beamline: PX14.2 / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 4, 2001 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→44.3 Å / Num. obs: 140877 / % possible obs: 99.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 20.935 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.053 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 4.1 / Num. unique all: 20513 / Rsym value: 0.185 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 549500 / Rmerge(I) obs: 0.053 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 99.9 % / Num. unique obs: 20513 / Num. measured obs: 76465 / Rmerge(I) obs: 0.185 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G1A Resolution: 1.8→500 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & HUber
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Displacement parameters | Biso mean: 23.5557 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→500 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 44.3 Å / σ(F): 0 / Rfactor obs: 0.205 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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