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Yorodumi- PDB-1g1a: THE CRYSTAL STRUCTURE OF DTDP-D-GLUCOSE 4,6-DEHYDRATASE (RMLB)FRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g1a | ||||||
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Title | THE CRYSTAL STRUCTURE OF DTDP-D-GLUCOSE 4,6-DEHYDRATASE (RMLB)FROM SALMONELLA ENTERICA SEROVAR TYPHIMURIUM | ||||||
Components | DTDP-D-GLUCOSE 4,6-DEHYDRATASE | ||||||
Keywords | LYASE / Rossmann fold / Protein-NAD complex / Short Chain Dehydrogenase | ||||||
Function / homology | Function and homology information dTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase activity / nucleotide-sugar metabolic process / O antigen biosynthetic process / dTDP-rhamnose biosynthetic process / extracellular polysaccharide biosynthetic process / NADH binding / lipopolysaccharide biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.47 Å | ||||||
Authors | Allard, S.T.M. / Giraud, M.-F. / Whitfield, C. / Graninger, M. / Messner, P. / Naismith, J.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: The crystal structure of dTDP-D-Glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar Typhimurium, the second enzyme in the dTDP-l-rhamnose pathway. Authors: Allard, S.T. / Giraud, M.F. / Whitfield, C. / Graninger, M. / Messner, P. / Naismith, J.H. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: The purifiaction, crystallisation and structural elucidation of dTDP-D-glucose 4,6-dehydratase (RmlB), the second enzyme of the dTDP-L-rhamnose synthesis pathway from Salmonella enterica serovar Typhimurium. Authors: Allard, S.T.M. / Giraud, M.-F. / Whitfield, C. / Messner, P. / 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 | 1g1a.cif.gz | 299.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g1a.ent.gz | 243.9 KB | Display | PDB format |
PDBx/mmJSON format | 1g1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/1g1a ftp://data.pdbj.org/pub/pdb/validation_reports/g1/1g1a | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological unit is a dimer. The assymmmetric unit contains two dimers. |
-Components
#1: Protein | Mass: 40767.516 Da / Num. of mol.: 4 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 / Variant: SEROVAR TYPHIMURIUM / Plasmid: PET28A(+) / Production host: Escherichia coli (E. coli) References: UniProt: P26391, UniProt: Q9EU31*PLUS, dTDP-glucose 4,6-dehydratase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-NAD / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.39 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 0.1M MES, 1.5M lithium Sulfate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.47→40.8 Å / Num. all: 74855 / Num. obs: 67669 / % possible obs: 90.4 % / Redundancy: 3 % / Biso Wilson estimate: 44.217 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.5 | |||||||||||||||
Reflection shell | Resolution: 2.47→2.56 Å / Redundancy: 2 % / Rmerge(I) obs: 0.358 / Num. unique all: 7903 / % possible all: 72.9 | |||||||||||||||
Reflection | *PLUS Num. measured all: 201143 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 72.9 % / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Resolution: 2.47→40.8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.47→40.8 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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