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- PDB-2wpb: Crystal structure of the E192N mutant of E. Coli N-acetylneuramin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wpb | ||||||
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Title | Crystal structure of the E192N mutant of E. Coli N-acetylneuraminic acid lyase in complex with pyruvate and the inhibitor (2R,3R)-2,3,4- trihydroxy-N,N-dipropylbutanamide in space group P21 crystal form I | ||||||
![]() | N-ACETYLNEURAMINATE LYASE | ||||||
![]() | LYASE / SUBSTRATE SPECIFICITY / CARBOHYDRATE METABOLISM / PROTEIN ENGINEERING / ALDOLASE / SCHIFF BASE | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Campeotto, I. / Bolt, A.H. / Harman, T.A. / Trinh, C.H. / Dennis, C.A. / Phillips, S.E.V. / Pearson, A.R. / Nelson, A. / Berry, A. | ||||||
![]() | ![]() Title: Structural Insights Into Substrate Specificity in Variants of N-Acetylneuraminic Acid Lyase Produced by Directed Evolution. Authors: Campeotto, I. / Bolt, A.H. / Harman, T.A. / Dennis, C.A. / Trinh, C.H. / Phillips, S.E.V. / Nelson, A. / Pearson, A.R. / Berry, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 246.7 KB | Display | ![]() |
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PDB format | ![]() | 199.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2wnnSC ![]() 2wnqC ![]() 2wnzC ![]() 2wo5C ![]() 2wsg 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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Unit cell |
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Components
#1: Protein | Mass: 33638.395 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-297 / Mutation: YES Source method: isolated from a genetically manipulated source Details: SCHIFF BASE BETWEEN LYS165 AND PYRUVATE IN ALL CHAINS Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZZI / ( #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLU 192 TO ASN ENGINEERED RESIDUE IN CHAIN B, GLU 192 TO ASN ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.81 % / Description: NONE |
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Crystal grow | pH: 8.2 / Details: 100MM TRIS-HCL PH 8.2, 200 MM NACL, 18% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: May 13, 2008 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.05→79.31 Å / Num. obs: 78597 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 24.528 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.6 | |||||||||||||||
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.6 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WNN Resolution: 2.05→71.88 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.827 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.038 / 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: 22.926 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→71.88 Å
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Refine LS restraints |
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