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Yorodumi- PDB-1kep: The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kep | ||||||
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Title | The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-xylose bound | ||||||
Components | dTDP-D-glucose 4,6-dehydratase | ||||||
Keywords | LYASE / Rossmann fold | ||||||
Function / homology | Function and homology information UDP-L-rhamnose synthase activity / UDP-glucose 4,6-dehydratase activity / UDP-rhamnose biosynthetic process / dTDP-glucose 4,6-dehydratase / flavonol biosynthetic process / dTDP-glucose 4,6-dehydratase activity / dTDP-rhamnose biosynthetic process / extracellular polysaccharide biosynthetic process / lipopolysaccharide biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Streptococcus suis (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 | 1kep.cif.gz | 171.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kep.ent.gz | 132.9 KB | Display | PDB format |
PDBx/mmJSON format | 1kep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/1kep ftp://data.pdbj.org/pub/pdb/validation_reports/ke/1kep | HTTPS FTP |
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-Related structure data
Related structure data | 1kerC 1ketC 1keuC 1kewC 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: 38982.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus suis (bacteria) / Gene: rmlB / Variant: serotype 2 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P95780, UniProt: Q8GIP9*PLUS, 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: 3.61 Å3/Da / Density % sol: 65.91 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 35% PEG 4000, 0.1M Citric acid pH 5.4, 0.3M ammonium sulphate and 3% 1,6-hexanediol, VAPOR DIFFUSION, HANGING DROP at 293K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop / Details: used microseeding | ||||||||||||||||||||||||||||||||||||||||||||||||
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: PX9.6 / Wavelength: 0.87 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 4, 2001 / Details: morrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→91.3 Å / Num. all: 102080 / Num. obs: 91826 / % possible obs: 97 % / Redundancy: 3.3 % / Biso Wilson estimate: 15.82 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.079 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 2.5 / Num. unique all: 12822 / Rsym value: 0.291 / % possible all: 85.1 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 102080 / % possible obs: 97 % / Num. measured all: 340418 / Rmerge(I) obs: 0.079 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 85.1 % / Num. unique obs: 12822 / Num. measured obs: 30104 / Rmerge(I) obs: 0.291 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 1G1A Resolution: 1.8→91.29 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: 6.427 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→91.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Software | *PLUS Name: REFMAC / Version: 5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 91.3 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.145 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.85 Å / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.225 |