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Yorodumi- PDB-8dak: Crystal structure of the GDP-D-glycero-4-keto-d-lyxo-heptose-3-ep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dak | ||||||||||||
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Title | Crystal structure of the GDP-D-glycero-4-keto-d-lyxo-heptose-3-epimerase from Campylobacter jejuni, serotype HS:3 | ||||||||||||
Components | GDP-D-glycero-4-keto-d-lyxo-heptose-3-epimerase | ||||||||||||
Keywords | ISOMERASE / 3-epimerase / campylobacter / capsular polysaccharide | ||||||||||||
Function / homology | dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase-related / dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / GUANOSINE-5'-DIPHOSPHATE / TETRAMETHYLAMMONIUM ION / dTDP-4-dehydrorhamnose 3,5-epimerase Function and homology information | ||||||||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||||||||
Authors | Thoden, J.B. / Ghosh, M.K. / Xiang, D.F. / Raushel, F.M. / Holden, H.M. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Biochemistry / Year: 2022 Title: C3- and C3/C5-Epimerases Required for the Biosynthesis of the Capsular Polysaccharides from Campylobacter jejuni . Authors: Ghosh, M.K. / Xiang, D.F. / 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 | 8dak.cif.gz | 101.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dak.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 8dak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dak_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8dak_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8dak_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 8dak_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/8dak ftp://data.pdbj.org/pub/pdb/validation_reports/da/8dak | HTTPS FTP |
-Related structure data
Related structure data | 8db5C 8dclC 8dcoC 7m14S S: Starting model for refinement C: citing same article (ref.) |
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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: 21189.135 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: serotype HS3 / Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: HS3.15, HS3/13/50.15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: F2X702, Isomerases #2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-TMA / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.37 Å3/Da / Density % sol: 48.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 10-12% PEG8000, 0.75 M tetramethylammonium chloride, 100 mM homopiperazine-1,4-bis(2-ethanesulfonic acid), pH 5.0, protein pre-incubated with 5 mM GDP |
-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: Jul 20, 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: 1.5→50 Å / Num. obs: 63904 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rsym value: 0.094 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.5→1.6 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 10456 / Rsym value: 0.369 / % possible all: 89.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 7M14 Resolution: 1.5→33.1 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.901 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.081 / 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: 57.05 Å2 / Biso mean: 9.26 Å2 / Biso min: 2.14 Å2
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Refinement step | Cycle: final / Resolution: 1.5→33.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.536 Å / Rfactor Rfree error: 0
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