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Yorodumi- PDB-5tpu: x-ray structure of the WlaRB TDP-quinovose 3,4-ketoisomerase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tpu | ||||||
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Title | x-ray structure of the WlaRB TDP-quinovose 3,4-ketoisomerase from campylobacter jejuni | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | ISOMERASE / ketoisomerase / quinovose / deoxy-sugar | ||||||
Function / homology | Function and homology information Sugar 3,4-ketoisomerase QdtA, cupin domain / WxcM-like, C-terminal / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Holden, H.M. / Thoden, J.B. / Li, J.Z. / Riegert, A.S. / Goneau, M.-F. / Cunningham, A.M. / Vinogradov, E. / Schoenhofen, I.C. / Gilbert, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Glycobiology / Year: 2017 Title: Characterization of the dTDP-Fuc3N and dTDP-Qui3N biosynthetic pathways in Campylobacter jejuni 81116. Authors: Li, Z.Z. / Riegert, A.S. / Goneau, M.F. / Cunningham, A.M. / Vinogradov, E. / Li, J. / Schoenhofen, I.C. / Thoden, J.B. / Holden, H.M. / Gilbert, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tpu.cif.gz | 129.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tpu.ent.gz | 100.2 KB | Display | PDB format |
PDBx/mmJSON format | 5tpu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/5tpu ftp://data.pdbj.org/pub/pdb/validation_reports/tp/5tpu | HTTPS FTP |
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-Related structure data
Related structure data | 5tpvC 2pa7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16061.453 Da / Num. of mol.: 4 / Mutation: E118A, K119A, E120A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Production host: Escherichia coli (E. coli) / Strain (production host): rosetta2(DE3) / References: UniProt: Q9ALS4 #2: Chemical | ChemComp-TYD / #3: Chemical | #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: 2.28 Å3/Da / Density % sol: 46.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES, 16-18% PEG-8000, 200 mM LiCl, 5 mM TDP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jul 16, 2016 / Details: montel |
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→50 Å / Num. obs: 39376 / % possible obs: 99.7 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.8 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PA7 Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.359 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.177 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.169 Å2
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Refinement step | Cycle: 1 / Resolution: 2→30 Å
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Refine LS restraints |
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