+Open data
-Basic information
Entry | Database: PDB / ID: 2ixi | ||||||
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Title | RmlC P aeruginosa with dTDP-xylose | ||||||
Components | DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE | ||||||
Keywords | ISOMERASE / LIPOPOLYSACCHARIDE BIOSYNTHESIS / EPIMERISE / EPIMERASE / EPIMERIZE | ||||||
Function / homology | Function and homology information dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / lipopolysaccharide core region biosynthetic process / extracellular polysaccharide biosynthetic process / lipopolysaccharide biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Dong, C. / Naismith, J.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Rmlc, a C3' and C5' Carbohydrate Epimerase, Appears to Operate Via an Intermediate with an Unusual Twist Boat Conformation. Authors: Dong, C. / Major, L.L. / Srikannathasan, V. / Errey, J.C. / Giraud, M.F. / Lam, J.S. / Graninger, M. / Messner, P. / Mcneil, M.R. / Field, R.A. / Whitfield, C. / 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 | 2ixi.cif.gz | 98.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ixi.ent.gz | 74.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ixi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/2ixi ftp://data.pdbj.org/pub/pdb/validation_reports/ix/2ixi | HTTPS FTP |
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-Related structure data
Related structure data | 2ixcC 2ixhC 2ixjSC 2ixkC 2ixlC 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: 21098.795 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9HU21 #2: Chemical | #3: Chemical | ChemComp-SRT / | #4: Water | ChemComp-HOH / | Sequence details | EXTRA SMS AT N-TERMINUS CLONING ARTEFACT | |
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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: 2.23 Å3/Da / Density % sol: 44.3 % |
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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 |
Detector | Type: ADSC CCD / Detector: CCD |
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→44 Å / Num. obs: 35190 / % possible obs: 80 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / % possible all: 67 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IXJ Resolution: 1.8→74.54 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.06 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.41 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→74.54 Å
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Refine LS restraints |
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