+Open data
-Basic information
Entry | Database: PDB / ID: 2ixh | ||||||
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Title | RmlC P aeruginosa with dTDP-rhamnose | ||||||
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: 2 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 | 2ixh.cif.gz | 97.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ixh.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ixh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/2ixh ftp://data.pdbj.org/pub/pdb/validation_reports/ix/2ixh | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21082.795 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: Water | ChemComp-HOH / | Sequence details | EXTRA S 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: 2.19 Å3/Da / Density % sol: 43.3 % |
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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: 2→40 Å / Num. obs: 30581 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→63.25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.909 / SU B: 9.215 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.184 / 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: 28.35 Å2
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Refinement step | Cycle: LAST / Resolution: 2→63.25 Å
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Refine LS restraints |
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