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Yorodumi- PDB-8ewu: X-ray structure of the GDP-6-deoxy-4-keto-D-lyxo-heptose-4-reduct... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ewu | ||||||||||||
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Title | X-ray structure of the GDP-6-deoxy-4-keto-D-lyxo-heptose-4-reductase from Campylobacter jejuni HS:15 | ||||||||||||
Components | GDP-L-fucose synthase | ||||||||||||
Keywords | BIOSYNTHETIC PROTEIN / OXIDOREDUCTASE / capsular polysaccharide / reductase | ||||||||||||
Function / homology | Function and homology information GDP-L-fucose synthase / GDP-L-fucose synthase activity / 'de novo' GDP-L-fucose biosynthetic process / NADP+ binding / isomerase activity Similarity search - Function | ||||||||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||||||||
Authors | Thoden, J.B. / Xiang, D.F. / Ghosh, M.K. / Riegert, A.S. / Raushel, F.M. / Holden, H.M. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Biochemistry / Year: 2023 Title: Bifunctional Epimerase/Reductase Enzymes Facilitate the Modulation of 6-Deoxy-Heptoses Found in the Capsular Polysaccharides of Campylobacter jejuni. Authors: Xiang, D.F. / Ghosh, M.K. / Riegert, A.S. / Thoden, J.B. / Holden, H.M. / Raushel, F.M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ewu.cif.gz | 179.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ewu.ent.gz | 138.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ewu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ewu_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8ewu_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8ewu_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 8ewu_validation.cif.gz | 53.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/8ewu ftp://data.pdbj.org/pub/pdb/validation_reports/ew/8ewu | HTTPS FTP |
-Related structure data
Related structure data | 7m13S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43171.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: HS:15 / Gene: fcl, HS15.12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2(DE3) / References: UniProt: F2X7A6, GDP-L-fucose synthase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.13 Å3/Da / Density % sol: 42.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein pre-incubated with 5.0 mM GDP, 5.0 mM NADPH. Precipitant: 18-22% PEG3350, 2% isopropanol, 100 mM HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Dec 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. obs: 121498 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rsym value: 0.049 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.45→1.55 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 20129 / Rsym value: 0.338 / % possible all: 87.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 7M13 Resolution: 1.45→33.38 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.782 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.24 Å2 / Biso mean: 16.068 Å2 / Biso min: 5 Å2
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Refinement step | Cycle: final / Resolution: 1.45→33.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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