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- PDB-1kbz: Crystal Structure of apo-dTDP-6-deoxy-L-lyxo-4-hexulose reductase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kbz | ||||||
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Title | Crystal Structure of apo-dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) from Salmonella enterica serovar Typhimurium | ||||||
![]() | dTDP-glucose oxidoreductase | ||||||
![]() | OXIDOREDUCTASE / Rossman-fold / sugar-nucleotide-binding domain | ||||||
Function / homology | ![]() methionine adenosyltransferase regulator activity / dTDP-4-dehydrorhamnose reductase / dTDP-4-dehydrorhamnose reductase activity / methionine adenosyltransferase complex / O antigen biosynthetic process / dTDP-rhamnose biosynthetic process / lipopolysaccharide biosynthetic process / S-adenosylmethionine biosynthetic process / extracellular polysaccharide biosynthetic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Blankenfeldt, W. / Kerr, I.D. / Giraud, M.F. / McMiken, H.J. / Leonard, G.A. / Whitfield, C. / Messner, P. / Graninger, M. / Naismith, J.H. | ||||||
![]() | ![]() Title: Variation on a theme of SDR. dTDP-6-deoxy-L- lyxo-4-hexulose reductase (RmlD) shows a new Mg2+-dependent dimerization mode. Authors: Blankenfeldt, W. / Kerr, I.D. / Giraud, M.F. / McMiken, H.J. / Leonard, G. / Whitfield, C. / Messner, P. / Graninger, M. / Naismith, J.H. #1: ![]() Title: Overexpression, purification, crystallisation and preliminary structural study of dTDP-6-deoxy-lyxo-4-reductase (RmlD) the fourth enzyme of the dTDP-rhanose synthesis pathway,from Salmonella ...Title: Overexpression, purification, crystallisation and preliminary structural study of dTDP-6-deoxy-lyxo-4-reductase (RmlD) the fourth enzyme of the dTDP-rhanose synthesis pathway,from Salmonella entrica serovar Typhimurim Authors: Giraud, M.F. / McMiken, H.J. / Leonard, G.A. / Messner, P. / Whitfield, C. / Naismith, J.H. #2: ![]() Title: The rhamnose pathway Authors: Giraud, M.F. / Naismith, J.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.5 KB | Display | ![]() |
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PDB format | ![]() | 55.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 402.6 KB | Display | ![]() |
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Full document | ![]() | 406 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 12.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a dimer generated by the the two-fold crystallographic c-axis: -x, -y, z. |
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Components
#1: Protein | Mass: 32589.943 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P26392, dTDP-4-dehydrorhamnose reductase |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.87 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: HEPES, PEG 4000, magnesium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP at 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.1 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→54.23 Å / Num. all: 14547 / Num. obs: 14547 / % possible obs: 99.4 % / Observed criterion σ(I): 2.9 / Redundancy: 11.8 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.21→2.27 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 2.9 / % possible all: 92 |
Reflection | *PLUS Num. measured all: 171243 / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS % possible obs: 92 % / Rmerge(I) obs: 0.249 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: BABINET MODEL WITH MASK. PARAMETERS FOR MASK CALCULATION: VDW PROBE RADIUS: 1.40; ION PROBE RADIUS: 0.80; SHRINKAGE RADIUS: 0.80 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.39 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→81.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.21→2.26 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 2.21 Å / Rfactor all: 0.1939 / Rfactor obs: 0.192 / Rfactor Rfree: 0.256 / Rfactor Rwork: 0.189 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.229 / Rfactor Rwork: 0.223 |