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Yorodumi- PDB-1eq2: THE CRYSTAL STRUCTURE OF ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eq2 | ||||||
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Title | THE CRYSTAL STRUCTURE OF ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE | ||||||
Components | ADP-L-GLYCERO-D-MANNOHEPTOSE 6-EPIMERASE | ||||||
Keywords | ISOMERASE / N-terminal domain Rossmann fold / C-terminal mixed alpha/beta domain / Short-chain dehydrogenase/reductase fold | ||||||
Function / homology | Function and homology information ADP-glyceromanno-heptose 6-epimerase / ADP-glyceromanno-heptose 6-epimerase activity / ADP-L-glycero-beta-D-manno-heptose biosynthetic process / lipopolysaccharide core region biosynthetic process / NADP+ binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Deacon, A.M. / Ni, Y.S. / Coleman Jr., W.G. / Ealick, S.E. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: The crystal structure of ADP-L-glycero-D-mannoheptose 6-epimerase: catalysis with a twist. Authors: Deacon, A.M. / Ni, Y.S. / Coleman Jr., W.G. / Ealick, S.E. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Crystallization and Preliminary X-ray Diffraction Studies of the Lipopolysaccharide Core Biosynthetic Enzyme ADP-L-glycero-D-mannoheptose 6-epimerase from Escherichia coli K-12 Authors: Ding, L. / Zhang, Y. / Deacon, A.M. / Ealick, S.E. / Ni, Y. / Sun, P. / Coleman Jr., W.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eq2.cif.gz | 621.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eq2.ent.gz | 513.1 KB | Display | PDB format |
PDBx/mmJSON format | 1eq2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/1eq2 ftp://data.pdbj.org/pub/pdb/validation_reports/eq/1eq2 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a pentamer. There are two pentamers in the asymmetric unit, each with a local non-crystallographic five-fold axis parallel to the crystallographic two-fold screw axis. |
-Components
#1: Protein | Mass: 34943.031 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PT7-5 / Production host: Escherichia coli (E. coli) References: UniProt: P67910, ADP-glyceromanno-heptose 6-epimerase #2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-ADQ / #4: 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: 2.83 Å3/Da / Density % sol: 56.61 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.0M ammonium sulphate, 2% PEG400, 0.1M HEPES buffer, 1mM ADP-glucose, 20nM spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: CHESS / Beamline: F1 / Wavelength: 0.919 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 22, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.919 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. all: 242386 / Num. obs: 242386 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.218 / Num. unique all: 239829 / % possible all: 78.6 |
Reflection | *PLUS Num. measured all: 573756 |
Reflection shell | *PLUS % possible obs: 78.6 % / Mean I/σ(I) obs: 3 |
-Processing
Software |
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Refinement | Resolution: 2→20 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 2 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.5 |