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Yorodumi- PDB-4bwl: Structure of the Y137A mutant of E. coli N-acetylneuraminic acid ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bwl | ||||||
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Title | Structure of the Y137A mutant of E. coli N-acetylneuraminic acid lyase in complex with pyruvate, N-acetyl-D-mannosamine and N- acetylneuraminic acid | ||||||
Components | (N-ACETYLNEURAMINATE ...) x 2 | ||||||
Keywords | LYASE / DIRECTED EVOLUTION / SUBSTRATE SPECIFICITY / PROTEIN ENGINEERING | ||||||
Function / homology | Function and homology information N-acetylneuraminate lyase / N-acetylneuraminate lyase activity / N-acetylneuraminate catabolic process / single-species biofilm formation / carbohydrate metabolic process / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Campeotto, I. / Phillips, S.E.V. / Pearson, A.R. / Nelson, A. / Berry, A. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2014 Title: The Reaction Mechanism of N-Acetylneuraminic Acid Lyase Revealed by a Combination of Crystallography, Qm/Mm Simulation and Mutagenesis. Authors: Daniels, A.D. / Campeotto, I. / Van Der Kamp, M.W. / Bolt, A.H. / Trinh, C.H. / Phillips, S.E.V. / Pearson, A.R. / Nelson, A. / Mulholland, A.J. / Berry, A. | ||||||
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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bwl.cif.gz | 235.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bwl.ent.gz | 188.6 KB | Display | PDB format |
PDBx/mmJSON format | 4bwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bwl_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 4bwl_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 4bwl_validation.xml.gz | 45.1 KB | Display | |
Data in CIF | 4bwl_validation.cif.gz | 61.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/4bwl ftp://data.pdbj.org/pub/pdb/validation_reports/bw/4bwl | HTTPS FTP |
-Related structure data
Related structure data | 2wnnS S: Starting model for refinement |
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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
-N-ACETYLNEURAMINATE ... , 2 types, 4 molecules ABDC
#1: Protein | Mass: 33492.273 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Details: SCHIFF BASE BETWEEN LYS165 AND N-ACETYLNEURAMINIC ACID Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PKNANA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6L4, N-acetylneuraminate lyase #2: Protein | | Mass: 33561.312 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: SCHIFF BASE BETWEEN LYS165 AND PYRUVATE / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PKNANA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6L4, N-acetylneuraminate lyase |
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-Sugars , 1 types, 3 molecules
#3: Sugar |
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-Non-polymers , 3 types, 105 molecules
#4: Chemical | #5: Chemical | ChemComp-MN9 / | #6: 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: 2.42 Å3/Da / Density % sol: 49.29 % / Description: NONE |
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Crystal grow | pH: 8.2 / Details: 100MM TRIS-HCL PH 8.2, 200MM NACL, 18% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 | |||||||||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 8, 2009 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2→49.5 Å / Num. obs: 82202 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.6 | |||||||||||||||
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.8 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WNN Resolution: 2→49.46 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.557 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2→49.46 Å
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