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- PDB-4utt: Structural characterisation of NanE, ManNac6P C2 epimerase, from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4utt | ||||||
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Title | Structural characterisation of NanE, ManNac6P C2 epimerase, from Clostridium perfingens | ||||||
![]() | (PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE) x 2 | ||||||
![]() | ISOMERASE / SUGAR 2-EPIMERASE / SIALIC ACID / SUGAR PHOSPHATE / ENZYME MECHANISM / CARBOHYDRATE / MUTAGENESIS / 1H NMR SPECTROSCOPY | ||||||
Function / homology | ![]() N-acetylmannosamine catabolic process / N-acylglucosamine-6-phosphate 2-epimerase / N-acylmannosamine-6-phosphate 2-epimerase activity / N-acylglucosamine-6-phosphate 2-epimerase activity / N-acetylmannosamine metabolic process / N-acetylneuraminate catabolic process / carbohydrate metabolic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pelissier, M.C. / Sebban-Kreuzer, C. / Guerlesquin, F. / Brannigan, J.A. / Davies, G.J. / Bourne, Y. / Vincent, F. | ||||||
![]() | ![]() 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. / Sebban-Kreuzer, C. / Guerlesquin, F. / Brannigan, J.A. / 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. THE SHEETS PRESENTED AS "CA" 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 "DA" 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 209.2 KB | Display | ![]() |
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PDB format | ![]() | 167.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 461.4 KB | Display | ![]() |
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Full document | ![]() | 469.4 KB | Display | |
Data in XML | ![]() | 46.2 KB | Display | |
Data in CIF | ![]() | 69.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4utuC ![]() 4utwC ![]() 1yxyS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25164.900 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: 8 CHLORIDE IONS AND 4 ACTETATE MOLECULES ARE BOUND TO THE 4 MONOMERS Source: (gene. exp.) ![]() Plasmid: PET-YSBLIC / Production host: ![]() ![]() References: UniProt: Q0TUP9, UniProt: Q8XNZ3*PLUS, N-acylglucosamine-6-phosphate 2-epimerase #2: Protein | Mass: 25113.832 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: 8 CHLORIDE IONS AND 4 ACTETATE MOLECULES ARE BOUND TO THE 4 MONOMERS Source: (gene. exp.) ![]() Plasmid: PET-YSBLIC / Production host: ![]() ![]() References: UniProt: Q0TUP9, UniProt: Q8XNZ3*PLUS, N-acylglucosamine-6-phosphate 2-epimerase #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-ACT / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.55 % / Description: NONE |
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Crystal grow | Details: 0.1 M NA CACODYLATE PH 6.5, 0.2 M CA ACETATE, 24.5% (W/V) PEG 2K MME AND 5% (V/V) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / 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: 1.71→41.45 Å / Num. obs: 48011 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.71→1.81 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2 / % possible all: 77 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1YXY Resolution: 1.71→82.2 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.259 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE LYS221 IS DISORDERED IN THE 4 MONOMERS
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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: 22.21 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→82.2 Å
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Refine LS restraints |
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