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Yorodumi- PDB-4utu: Structural and biochemical characterization of the N- acetylmanno... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4utu | ||||||
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Title | Structural and biochemical characterization of the N- acetylmannosamine-6-phosphate 2-epimerase from Clostridium perfringens | ||||||
Components | N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE | ||||||
Keywords | ISOMERASE / SUGAR 2-EPIMERASE / SIALIC ACID / SUGAR PHOSPHATE / ENZYME MECHANISM / CARBOHYDRATE / MUTAGENESIS / 1H NMR SPECTROSCOPY | ||||||
Function / homology | Function and homology information N-acetylmannosamine catabolic process / N-acylglucosamine-6-phosphate 2-epimerase / : / N-acylglucosamine-6-phosphate 2-epimerase activity / N-acetylneuraminate catabolic process / carbohydrate metabolic process / cytosol Similarity search - Function | ||||||
Biological species | CLOSTRIDIUM PERFRINGENS STR. 13 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Pelissier, M.C. / Sebban-Kreuzer, C. / Guerlesquin, F. / Brannigan, J.A. / Davies, G.J. / Bourne, Y. / Vincent, F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Structural and Functional Characterization of the Clostridium Perfringens N-Acetylmannosamine-6-Phosphate 2-Epimerase Essential for the Sialic Acid Salvage Pathway Authors: Pelissier, M.C. / Sebban-Kreuzer, C. / Guerlesquin, F. / Brannigan, J.A. / Davies, G.J. / Bourne, Y. / Vincent, F. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4utu.cif.gz | 199 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4utu.ent.gz | 161.6 KB | Display | PDB format |
PDBx/mmJSON format | 4utu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4utu_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4utu_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4utu_validation.xml.gz | 24 KB | Display | |
Data in CIF | 4utu_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/4utu ftp://data.pdbj.org/pub/pdb/validation_reports/ut/4utu | HTTPS FTP |
-Related structure data
Related structure data | 4uttSC 4utwC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25055.730 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-ACETYLMANNOSAMINE-6-PHOSPHATE BOUND TO MOLECULE A AND B Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS STR. 13 (bacteria) Plasmid: PET-YSBLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA References: UniProt: Q8XNZ3, N-acylglucosamine-6-phosphate 2-epimerase #2: Chemical | #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: 2.36 Å3/Da / Density % sol: 47.92 % / Description: NONE |
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Crystal grow | Details: 0.1 M PROPIONIC ACID, CACODYLATE, BIS-TRIS PROPANE BUFFER PH 8.0 AND 25% (W/V) PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→41.1 Å / Num. obs: 78204 / % possible obs: 99.3 % / Observed criterion σ(I): 4.3 / Redundancy: 7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.3 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4UTT Resolution: 1.45→42 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.745 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LYS 221 IS DISORDERED
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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 WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.602 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→42 Å
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Refine LS restraints |
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