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Yorodumi- PDB-1bws: CRYSTAL STRUCTURE OF GDP-4-KETO-6-DEOXY-D-MANNOSE EPIMERASE/REDUC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bws | ||||||
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Title | CRYSTAL STRUCTURE OF GDP-4-KETO-6-DEOXY-D-MANNOSE EPIMERASE/REDUCTASE FROM ESCHERICHIA COLI A KEY ENZYME IN THE BIOSYNTHESIS OF GDP-L-FUCOSE | ||||||
Components | PROTEIN (GDP-4-KETO-6-DEOXY-D-MANNOSE EPIMERASE/REDUCTASE) | ||||||
Keywords | OXIDOREDUCTASE / EPIMERASE/REDUCTASE / GDP-L-FUCOSE BIOSYNTHESIS | ||||||
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 / MIR / Resolution: 2.2 Å | ||||||
Authors | Rizzi, M. / Tonetti, M. / Flora, A.D. / Bolognesi, M. | ||||||
Citation | Journal: Structure / Year: 1998 Title: GDP-4-keto-6-deoxy-D-mannose epimerase/reductase from Escherichia coli, a key enzyme in the biosynthesis of GDP-L-fucose, displays the structural characteristics of the RED protein homology superfamily. Authors: Rizzi, M. / Tonetti, M. / Vigevani, P. / Sturla, L. / Bisso, A. / Flora, A.D. / Bordo, D. / Bolognesi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bws.cif.gz | 77.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bws.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 1bws.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bws_validation.pdf.gz | 473.1 KB | Display | wwPDB validaton report |
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Full document | 1bws_full_validation.pdf.gz | 483.8 KB | Display | |
Data in XML | 1bws_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 1bws_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/1bws ftp://data.pdbj.org/pub/pdb/validation_reports/bw/1bws | HTTPS FTP |
-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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-Components
#1: Protein | Mass: 36173.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P32055 |
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#2: Chemical | ChemComp-NDP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.57 % | ||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||
Crystal | *PLUS Density % sol: 64 % | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / Num. obs: 24481 / % possible obs: 99.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 13.6 |
Reflection | *PLUS Num. measured all: 105130 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.2→15 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / σ(F): 0 / Rfactor obs: 0.202 / Rfactor Rfree: 0.287 / Rfactor Rwork: 0.202 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_deg / Dev ideal: 1.65 |