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Yorodumi- PDB-8dcl: Crystal structure of the GDP-D-glycero-4-keto-D-lyxo-heptose-3-ep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dcl | ||||||||||||
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Title | Crystal structure of the GDP-D-glycero-4-keto-D-lyxo-heptose-3-epimerase from campylobacter jejuni, serotype HS:23/36 | ||||||||||||
Components | GDP-D-glycero-4-keto-D-lyxo-heptose-3-epimerase | ||||||||||||
Keywords | ISOMERASE / 3-epimerase / Campylobacter / capsular polysaccharide | ||||||||||||
Function / homology | Function and homology information dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / extracellular polysaccharide biosynthetic process / cytosol Similarity search - Function | ||||||||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 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 | 8dcl.cif.gz | 101.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dcl.ent.gz | 73.9 KB | Display | PDB format |
PDBx/mmJSON format | 8dcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dcl_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8dcl_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8dcl_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 8dcl_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/8dcl ftp://data.pdbj.org/pub/pdb/validation_reports/dc/8dcl | HTTPS FTP |
-Related structure data
Related structure data | 8dakC 8db5C 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 21898.908 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: serotype HS:23/36 / Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: BBR99_05345, F1P94_09915, HS23.15 / Variant: serotype HS:23/36 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 References: UniProt: Q6EF58, dTDP-4-dehydrorhamnose 3,5-epimerase |
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-Non-polymers , 5 types, 411 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.08 Å3/Da / Density % sol: 40.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Protein incubated with 5 mM GDP; precipitant: 18-20% PEG3350, 200 mM potassium chloride, 100 mM HEPES, pH 8.0 |
-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 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 48120 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.049 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.55→1.65 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 7423 / Rsym value: 0.258 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 7M14 Resolution: 1.55→35.75 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.833 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.089 / 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: 59.76 Å2 / Biso mean: 15.814 Å2 / Biso min: 6.86 Å2
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Refinement step | Cycle: final / Resolution: 1.55→35.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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