[English] 日本語
Yorodumi- PDB-1kc1: Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (Rm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kc1 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH | ||||||
Components | dTDP-glucose oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / Rossman-fold / sugar-nucleotide-binding domain | ||||||
Function / homology | Function and homology information dTDP-4-dehydrorhamnose reductase / dTDP-4-dehydrorhamnose reductase activity / O antigen biosynthetic process / dTDP-rhamnose biosynthetic process / extracellular polysaccharide biosynthetic process / lipopolysaccharide biosynthetic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1kc1.cif.gz | 74.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1kc1.ent.gz | 55.4 KB | Display | PDB format |
PDBx/mmJSON format | 1kc1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/1kc1 ftp://data.pdbj.org/pub/pdb/validation_reports/kc/1kc1 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
| ||||||||||||
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 |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-NDP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.93 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 6, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→39.84 Å / Num. all: 8506 / Num. obs: 8506 / % possible obs: 99.1 % / Observed criterion σ(I): 1.6 / Redundancy: 4.2 % / Biso Wilson estimate: 70 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 1.6 / % possible all: 99.4 |
Reflection | *PLUS Num. measured all: 38031 / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 99.4 % / Rmerge(I) obs: 0.475 |
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.6→81.65 Å / SU B: 16.868 / SU ML: 0.365 / SU Rfree: 0.351 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.351 / Stereochemistry target values: Engh & Huber Details: TLS-refinement with 3 TLS-bodies (cofactor-binding domain, substrate-binding domain, waters) throughout
| ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.35 Å2
| ||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.354 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→81.65 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.67 Å / Total num. of bins used: 20 /
| ||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.173 / Rfactor Rfree: 0.251 / Rfactor Rwork: 0.169 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.366 / Rfactor Rwork: 0.244 |