+Open data
-Basic information
Entry | Database: PDB / ID: 7pwi | ||||||||||||
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Title | Structure of the dTDP-sugar epimerase StrM | ||||||||||||
Components | dTDP-4-keto-rhamnose 3,5-epimerase,dTDP-4-dehydrorhamnose 3,5-epimerase | ||||||||||||
Keywords | SUGAR BINDING PROTEIN / Coxiella burnetii / O-antigen / epimerase / enzyme kinetics | ||||||||||||
Function / homology | Function and homology information streptomycin biosynthetic process / dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / carbohydrate metabolic process Similarity search - Function | ||||||||||||
Biological species | Streptomyces griseus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.326 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 | 7pwi.cif.gz | 69.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pwi.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7pwi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pwi_validation.pdf.gz | 434 KB | Display | wwPDB validaton report |
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Full document | 7pwi_full_validation.pdf.gz | 435.8 KB | Display | |
Data in XML | 7pwi_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 7pwi_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/7pwi ftp://data.pdbj.org/pub/pdb/validation_reports/pw/7pwi | HTTPS FTP |
-Related structure data
Related structure data | 7pviC 7pwbC 7pwhC 4hmzS C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 35205.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces griseus (bacteria) / Gene: strM / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P29783, dTDP-4-dehydrorhamnose 3,5-epimerase |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.24 % |
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Crystal grow | Temperature: 291 K / Method: microbatch Details: 10% PEG 6,000, 30% PEG 300, 100 mM CaCl2, 50 mM Tris pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.326→66.18 Å / Num. obs: 36601 / % possible obs: 74 % / Redundancy: 6.3 % / CC1/2: 0.996 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.326→1.433 Å / Num. unique obs: 1824 / CC1/2: 0.304 / % possible all: 20.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HMZ Resolution: 1.326→66.18 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.341 / SU ML: 0.053 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.084 / Details: Hydrogens have not been used
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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: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.358 Å2
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Refinement step | Cycle: LAST / Resolution: 1.326→66.18 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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