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- PDB-2wo5: Structure of wild type E. coli N-acetylneuraminic acid lyase in s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wo5 | ||||||
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Title | Structure of wild type E. coli N-acetylneuraminic acid lyase in space group P21 crystal form I | ||||||
![]() | N-ACETYLNEURAMINATE LYASE | ||||||
![]() | LYASE / SUBSTRATE SPECIFICITY / CARBOHYDRATE METABOLISM / DIRECTED EVOLUTION / 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 | ![]() | 231.8 KB | Display | ![]() |
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PDB format | ![]() | 188.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.3 KB | Display | ![]() |
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Full document | ![]() | 485.1 KB | Display | |
Data in XML | ![]() | 45.1 KB | Display | |
Data in CIF | ![]() | 63.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wnnSC ![]() 2wnqC ![]() 2wnzC ![]() 2wpbC ![]() 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: 33584.367 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-297 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.85 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 100MM TRIS-HCL PH 8.0, 200MM NACL, 18% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 25, 2008 | |||||||||||||||
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: 2.2→79.56 Å / Num. obs: 61635 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.6 | |||||||||||||||
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WNN Resolution: 2.2→71.09 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / SU B: 9.361 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.051 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.076 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→71.09 Å
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Refine LS restraints |
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