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Yorodumi- PDB-1kc3: Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (Rm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kc3 | ||||||
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Title | Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH and dTDP-L-rhamnose | ||||||
Components | dTDP-glucose oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / Rossman-fold / sugar-nucleotide-binding domain | ||||||
Function / homology | Function and homology information 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 | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å | ||||||
Authors | Blankenfeldt, W. / Kerr, I.D. / Giraud, M.F. / McMiken, H.J. / Leonard, G.A. / Whitfield, C. / Messner, P. / Graninger, M. / Naismith, J.H. | ||||||
Citation | Journal: Structure / Year: 2002 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: Journal: Acta Crystallogr.,Sect.D / Year: 1999 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: Journal: Curr.Opin.Struct.Biol. / Year: 2000 Title: The rhamnose pathway Authors: Giraud, M.F. / 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 | 1kc3.cif.gz | 77.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kc3.ent.gz | 56.6 KB | Display | PDB format |
PDBx/mmJSON format | 1kc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kc3_validation.pdf.gz | 924.4 KB | Display | wwPDB validaton report |
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Full document | 1kc3_full_validation.pdf.gz | 937.6 KB | Display | |
Data in XML | 1kc3_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 1kc3_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/1kc3 ftp://data.pdbj.org/pub/pdb/validation_reports/kc/1kc3 | HTTPS FTP |
-Related structure data
-Links
-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 twofold axis along c: -x, -y, z. |
-Components
#1: Protein | Mass: 32589.943 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: rfbA / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(lambda DE3)pLysS References: UniProt: P26392, dTDP-4-dehydrorhamnose reductase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-NDP / |
#4: Chemical | ChemComp-TRH / |
#5: 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: 2.2 Å3/Da / Density % sol: 44.04 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: HEPES, PEG-MME 5000, MgCl2, pH 6.8, 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: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 27, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→28.75 Å / Num. all: 7905 / Num. obs: 7905 / % possible obs: 99.1 % / Observed criterion σ(I): 1.8 / Redundancy: 3.5 % / Biso Wilson estimate: 66 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 1.8 / % possible all: 99.3 |
Reflection | *PLUS Num. measured all: 28521 / Rmerge(I) obs: 0.105 |
Reflection shell | *PLUS % possible obs: 99.3 % / Rmerge(I) obs: 0.377 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.7→28.87 Å / SU B: 18.382 / SU ML: 0.364 / SU Rfree: 0.449 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.449 / Stereochemistry target values: Engh & Huber Details: TLS-option with cofactor-binding, substrate-binding domains and waters as three separate TLS-bodies was used throughout
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Displacement parameters | Biso mean: 39.02 Å2
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Refine analyze | Luzzati coordinate error free: 0.449 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→28.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Rfactor all: 0.198697 / Rfactor obs: 0.196 / Rfactor Rfree: 0.289 / Rfactor Rwork: 0.191 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.291 / Rfactor Rwork: 0.213 |