+Open data
-Basic information
Entry | Database: PDB / ID: 1dzt | ||||||
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Title | RMLC FROM SALMONELLA TYPHIMURIUM | ||||||
Components | DTDP-4-DEHYDRORHAMNOSE 3\,5-EPIMERASE | ||||||
Keywords | ISOMERASE / 3\ / 5 HEXULOSE EPIMERASE | ||||||
Function / homology | Function and homology information dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / O antigen biosynthetic process / dTDP-rhamnose biosynthetic process / : / lipopolysaccharide biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | SALMONELLA TYPHIMURIUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Naismith, J.H. / Giraud, M.F. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 Title: Rmlc, the Third Enzyme of Dtdp-L-Rhamnose Pathway, is a New Class of Epimerase. Authors: Giraud, M.F. / Leonard, G.A. / Field, R.A. / Berlind, 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 | 1dzt.cif.gz | 94.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dzt.ent.gz | 72 KB | Display | PDB format |
PDBx/mmJSON format | 1dzt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dzt_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1dzt_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1dzt_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 1dzt_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/1dzt ftp://data.pdbj.org/pub/pdb/validation_reports/dz/1dzt | HTTPS FTP |
-Related structure data
Related structure data | 1dzrSC S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.04177, 0.79933, -0.59943), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 20684.373 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 References: UniProt: P26394, dTDP-4-dehydrorhamnose 3,5-epimerase |
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-Non-polymers , 5 types, 327 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-TPE / | #5: Chemical | ChemComp-ATY / | #6: Water | ChemComp-HOH / | |
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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: 3.32 Å3/Da / Density % sol: 62.93 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.75 / Method: vapor diffusion, sitting drop / Details: Giraud, M.-F., (1999) Acta Crystallogr, D55, 706. | ||||||||||||||||||||||||||||||
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: SRS / Beamline: PX9.6 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 28562 / % possible obs: 99 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 30.7 |
Reflection | *PLUS Lowest resolution: 3 Å / % possible obs: 98.9 % / Redundancy: 4.2 % |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / % possible obs: 99.8 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 6.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DZR Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 40 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.0088 |