+Open data
-Basic information
Entry | Database: PDB / ID: 1e6u | ||||||
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Title | GDP 4-keto-6-deoxy-D-mannose epimerase reductase | ||||||
Components | GDP-FUCOSE SYNTHETASE | ||||||
Keywords | EPIMERASE/REDUCTASE / SDR / RED / EPIMERASE-REDUCTASE complex | ||||||
Function / homology | Function and homology information GDP-L-fucose synthase / GDP-L-fucose synthase activity / colanic acid biosynthetic process / 'de novo' GDP-L-fucose biosynthetic process / NADP+ binding / isomerase activity / protein homodimerization activity / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Rosano, C. / Izzo, G. / Bolognesi, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Probing the Catalytic Mechanism of Gdp-4-Keto-6-Deoxy-D-Mannose Epimerase/Reductase by Kinetic and Crystallographic Characterization of Site-Specific Mutants Authors: Rosano, C. / Bisso, A. / Izzo, G. / Tonetti, M. / Sturla, L. / De Flora, A. / Bolognesi, M. #1: Journal: Croatica Chemica Acta / Year: 2000 Title: The High Resolution Structure of Gdp 4-Keto-6-Deoxy-D-Mannose Epimerase/Reductase Authors: Rosano, C. / Izzo, G. / Sturla, L. / Bisso, A. / Tonetti, M. / Bolognesi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e6u.cif.gz | 91.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e6u.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 1e6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/1e6u ftp://data.pdbj.org/pub/pdb/validation_reports/e6/1e6u | HTTPS FTP |
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-Related structure data
Related structure data | 1e7qC 1e7rC 1e7sC 1bwsS 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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Components on special symmetry positions |
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Details | BIOLOGICAL_UNIT: DIMERIC |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36186.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: UNKNOWN MOLECULE LABELED AS ACETYLPHOSPHATE / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P32055, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives |
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-Non-polymers , 5 types, 379 molecules
#2: Chemical | ChemComp-NAP / | ||||
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#3: Chemical | ChemComp-UVW / | ||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-TRS / | #6: Water | ChemComp-HOH / | |
-Details
Compound details | FUNCTION: TWO STEP NADP-DEPENDENT CONVERSION OF GDP-4-DEHYDRO-6- DEOXY-D-MANNOSE TO GDP-FUCOSE. ...FUNCTION: TWO STEP NADP-DEPENDENT CONVERSION |
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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: 3.16 Å3/Da / Density % sol: 61.04 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / pH: 6.5 Details: 1.5 M LITHIUM SULPHATE, PH 6.5 0.1M TRIS BUFFER 21C | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / Method: unknown / PH range low: 7.8 / PH range high: 6.5 | ||||||||||||||||||||||||
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: ELETTRA / Beamline: 5.2R / Wavelength: 0.855 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.855 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→100 Å / Num. obs: 80994 / % possible obs: 99.1 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.45→1.48 Å / Mean I/σ(I) obs: 5.5 / % possible all: 99 |
Reflection shell | *PLUS % possible obs: 99 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BWS Resolution: 1.45→10 Å / SU B: 0.66156 / SU ML: 0.02616 / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.049
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Refinement step | Cycle: LAST / Resolution: 1.45→10 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.167 / Rfactor Rwork: 0.127 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |