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Yorodumi- PDB-1n2s: CRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n2s | |||||||||
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Title | CRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RMLD) IN COMPLEX WITH NADH | |||||||||
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 enterica subsp. enterica serovar Typhimurium (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 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 Mg(2+)-Dependent Dimerization Mode Authors: Blankenfeldt, W. / Kerr, I.D. / Giraud, M.F. / McMiken, H.J. / Leonard, G.A. / 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 | 1n2s.cif.gz | 76.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n2s.ent.gz | 56.3 KB | Display | PDB format |
PDBx/mmJSON format | 1n2s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n2s_validation.pdf.gz | 735.1 KB | Display | wwPDB validaton report |
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Full document | 1n2s_full_validation.pdf.gz | 741.6 KB | Display | |
Data in XML | 1n2s_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 1n2s_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/1n2s ftp://data.pdbj.org/pub/pdb/validation_reports/n2/1n2s | 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 from the 2-fold crystallographic axis |
-Components
#1: Protein | Mass: 32589.943 Da / Num. of mol.: 1 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: RFBA / Plasmid: PET30A / 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-NAI / |
#4: Chemical | ChemComp-TRS / |
#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: 2.14 Å3/Da / Density % sol: 42.57 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Tris, PEG 4000, MgCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP at 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 19, 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→54.23 Å / Num. obs: 19137 / % possible obs: 99.8 % / Observed criterion σ(I): 1.5 / Redundancy: 4.7 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 1.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→81.7 Å / Cross valid method: THROUGHOUT / σ(F): 0 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: 28.46 Å2
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Refinement step | Cycle: LAST / Resolution: 2→81.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å /
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