+Open data
-Basic information
Entry | Database: PDB / ID: 7pvi | ||||||||||||
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Title | dTDP-sugar epimerase | ||||||||||||
Components | dTDP-4-dehydrorhamnose 3,5-epimerase | ||||||||||||
Keywords | SUGAR BINDING PROTEIN / Coxiella burnetii / O-antigen / epimerase / enzyme kinetics | ||||||||||||
Function / homology | Function and homology information : / racemase and epimerase activity / dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / extracellular polysaccharide biosynthetic process / cytosol Similarity search - Function | ||||||||||||
Biological species | Coxiella burnetii (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.434 Å | ||||||||||||
Authors | Cross, A.R. / Harmer, N.J. / Isupov, M.N. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: Spinning sugars in antigen biosynthesis: characterization of the Coxiella burnetii and Streptomyces griseus TDP-sugar epimerases. Authors: Cross, A.R. / Roy, S. / Vivoli Vega, M. / Rejzek, M. / Nepogodiev, S.A. / Cliff, M. / Salmon, D. / Isupov, M.N. / Field, R.A. / Prior, J.L. / Harmer, N.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pvi.cif.gz | 119.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pvi.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7pvi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/7pvi ftp://data.pdbj.org/pub/pdb/validation_reports/pv/7pvi | HTTPS FTP |
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-Related structure data
Related structure data | 7pwbC 7pwhC 7pwiC 2ixiS 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: -2 - 187 / Label seq-ID: 20 - 209
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
-Protein , 1 types, 2 molecules AAABBB
#1: Protein | Mass: 24486.916 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxiella burnetii (strain RSA 493 / Nine Mile phase I) (bacteria) Strain: RSA 493 / Nine Mile phase I / Gene: rfbC, CBU_1838 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q83AP3, dTDP-4-dehydrorhamnose 3,5-epimerase |
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-Sugars , 2 types, 4 molecules
#2: Sugar | #3: Sugar | |
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-Non-polymers , 3 types, 460 molecules
#4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-FLC / | #6: Water | ChemComp-HOH / | |
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-Details
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: 48.02 % |
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Crystal grow | Temperature: 291 K / Method: microbatch Details: 1.0 M sodium citrate tribasic dihydrate, 0.1 M sodium cacodylate pH 6.5) Crystal was soaked in 15% w/v of D-xylose |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.434→51.39 Å / Num. obs: 54843 / % possible obs: 65.9 % / Redundancy: 3.3 % / CC1/2: 0.999 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.434→1.605 Å / Num. unique obs: 2742 / CC1/2: 0.585 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IXI Resolution: 1.434→51.39 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.753 / SU ML: 0.062 / Cross valid method: FREE R-VALUE / ESU R: 0.094 / ESU R Free: 0.093 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.918 Å2
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Refinement step | Cycle: LAST / Resolution: 1.434→51.39 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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