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- PDB-4ah7: Structure of Wild Type Stapylococcus aureus N-acetylneuraminic ac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ah7 | ||||||
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Title | Structure of Wild Type Stapylococcus aureus N-acetylneuraminic acid lyase in complex with pyruvate | ||||||
![]() | N-ACETYLNEURAMINATE LYASE | ||||||
![]() | LYASE | ||||||
Function / homology | ![]() N-acetylneuraminate lyase / N-acetylneuraminate lyase activity / N-acetylneuraminate catabolic process / carbohydrate metabolic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Timms, N. / Poyakova, A. / Windle, C.L. / Trinh, C.H. / Nelson, A. / Pearson, A.R. / Berry, A. | ||||||
![]() | ![]() Title: Structural Insights Into the Recovery of Aldolase Activity in N-Acetylneuraminic Acid Lyase by Replacement of the Catalytically Active Lysine with Gamma-Thialysine by Using a Chemical Mutagenesis Strategy. Authors: Timms, N. / Windle, C.L. / Polyakova, A. / Ault, J.R. / Trinh, C.H. / Pearson, A.R. / Nelson, A. / 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 225.6 KB | Display | ![]() |
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PDB format | ![]() | 190 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.8 KB | Display | ![]() |
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Full document | ![]() | 462.6 KB | Display | |
Data in XML | ![]() | 40.9 KB | Display | |
Data in CIF | ![]() | 57.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ahoC ![]() 4ahpC ![]() 4ahqC ![]() 4amaC ![]() 4ah8 C: citing same article ( |
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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: 33843.184 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: LYSINE AT POSITION 165 IS BOUND WITH PYRUVATE THROUGH SCHIFF BASE Source: (gene. exp.) ![]() Plasmid: PKK223-3 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | Details: 200 MM NACL, 100 MM TRIS HCL PH 7.4, 28% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 16, 2011 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→58.91 Å / Num. obs: 53415 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.3→54.93 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.882 / SU B: 7.576 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.402 / ESU R Free: 0.261 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.902 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→54.93 Å
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Refine LS restraints |
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