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Yorodumi- PDB-8syb: X-ray crystal structure of UDP-2,3-diacetamido-2,3-dideoxy-glucur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8syb | ||||||
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Title | X-ray crystal structure of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase from Thermus thermophilus strain HB27, D98N variant in the presence of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid and UDP-N-acetylglucosamine at pH 9 | ||||||
Components | UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase | ||||||
Keywords | ISOMERASE / lipopolysaccharide / O-antigen / 2-epimerase | ||||||
Function / homology | UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) / UDP-N-acetylglucosamine 2-epimerase WecB-like / UDP-N-acetylglucosamine 2-epimerase domain / UDP-N-acetylglucosamine 2-epimerase / UDP-N-acetylglucosamine 2-epimerase activity / nucleotide binding / Chem-MJL / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / UDP-N-acetylglucosamine 2-epimerase Function and homology information | ||||||
Biological species | Thermus thermophilus HB27 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kroft, C.W. / Thoden, J.B. / Holden, H.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Structural analysis of a bacterial UDP-sugar 2-epimerase reveals the active site architecture before and after catalysis. Authors: Thoden, J.B. / McKnight, J.O. / Kroft, C.W. / Jast, J.D.T. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8syb.cif.gz | 165.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8syb.ent.gz | 127.7 KB | Display | PDB format |
PDBx/mmJSON format | 8syb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8syb_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8syb_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8syb_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | 8syb_validation.cif.gz | 41.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sy/8syb ftp://data.pdbj.org/pub/pdb/validation_reports/sy/8syb | HTTPS FTP |
-Related structure data
Related structure data | 8sxvC 8sxwC 8sxyC 8sy0C 8sy9C 8syaC 8sydC 8syeC 8syhC 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: 41994.086 Da / Num. of mol.: 2 / Mutation: D98N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Strain: ATCC BAA-163 / DSM 7039 / HB27 / Gene: TT_C0285 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q72KY0 |
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-Non-polymers , 5 types, 233 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-NA / | #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: 2.29 Å3/Da / Density % sol: 46.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: protein incubated with 5 mM UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid and 5 mM UDP-N-acetyl-glucosamine. Precipitant used was 18-22% poly(ethylene glycol) 8000, 200 mM KCl, 100 mM CHES (pH9) |
-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: Feb 22, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 38034 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rsym value: 0.084 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3.7 % / Num. unique obs: 4689 / R split: 2.3 / Rsym value: 0.38 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→44.79 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.882 / SU B: 8.679 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.16 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→44.79 Å
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