+Open data
-Basic information
Entry | Database: PDB / ID: 1e7q | ||||||
---|---|---|---|---|---|---|---|
Title | GDP 4-keto-6-deoxy-D-mannose epimerase reductase S107A | ||||||
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: 1.6 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1e7q.cif.gz | 88.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1e7q.ent.gz | 64.5 KB | Display | PDB format |
PDBx/mmJSON format | 1e7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/1e7q ftp://data.pdbj.org/pub/pdb/validation_reports/e7/1e7q | HTTPS FTP |
---|
-Related structure data
Related structure data | 1e6uC 1e7rC 1e7sC 1bwsS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36128.078 Da / Num. of mol.: 1 / Mutation: YES 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 |
---|
-Non-polymers , 5 types, 321 molecules
#2: Chemical | ChemComp-NAP / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-UVW / | ||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-TRS / | #6: Water | ChemComp-HOH / | |
-Details
Compound details | CHAIN A ENGINEERED MUTATION SER107ALA NADP-DEPENDENT CONVERSION OF GDP-4-DEHYDRO-6-DEOXY-D-MANNOSE ...CHAIN A ENGINEERED |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.53 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.844 |
Detector | Type: MARRESEARCH |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.844 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→100 Å / Num. obs: 61196 / % possible obs: 99.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 9.65 |
Reflection shell | Resolution: 1.6→1.63 Å / Mean I/σ(I) obs: 2.4 / % possible all: 99.1 |
Reflection shell | *PLUS % possible obs: 99.1 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BWS Resolution: 1.6→10 Å / SU B: 1.13 / SU ML: 0.04 / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.07
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|