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- PDB-5a8g: Crystal structure of the wild-type Staphylococcus aureus N- acety... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a8g | ||||||
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Title | Crystal structure of the wild-type Staphylococcus aureus N- acetylneurminic acid lyase in complex with fluoropyruvate | ||||||
![]() | 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 | ![]() ![]() ![]() | ||||||
![]() | Stockwell, J. / Daniels, A.D. / Windle, C.L. / Harman, T. / Woodhall, T. / Trinh, C.H. / Lebel, T. / Pearson, A.R. / Mulholland, K. / Berry, A. / Nelson, A. | ||||||
![]() | ![]() Title: Evaluation of Fluoropyruvate as Nucleophile in Reactions Catalysed by N-Acetyl Neuraminic Acid Lyase Variants: Scope, Limitations and Stereoselectivity. Authors: Stockwell, J. / Daniels, A.D. / Windle, C.L. / Harman, T.A. / Woodhall, T. / Lebl, T. / Trinh, C.H. / Mulholland, K. / Pearson, A.R. / Berry, A. / Nelson, A. | ||||||
History |
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Remark 700 | THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL ... 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. SHEET DETERMINATION METHOD: DSSP 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 239.9 KB | Display | ![]() |
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PDB format | ![]() | 196.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4ahpS 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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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.8514, 0.004464, -0.5244), Vector: |
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Components
#1: Protein | Mass: 34121.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: SCHIFF BASE BETWEEN K165 AND FLUOROPYRUVATE Source: (gene. exp.) ![]() Description: STANDARD LABORATORY STRAIN / Plasmid: PKK223-3 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | Nonpolymer details | (2S)-2-AMINO-5-[(1-CARBOXY-2-FLUOROETHYL)AMINO]PENTANOIC ACID (KPF): FLUOROPYRUVATE COVALENTLY ...(2S)-2-AMINO-5-[(1-CARBOXY-2-FLUOROETHY | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.36 % / Description: NONE |
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Crystal grow | Details: 200MM NACL, 100MM TRIS/HCL PH 7.0-8.5, 18-28% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2012 / Details: MIRRORS |
Radiation | Monochromator: SI(111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→28.89 Å / Num. obs: 70045 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.71→1.8 Å / Redundancy: 8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.4 / % possible all: 91 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4AHP Resolution: 1.72→75.2 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.569 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.102 / 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: 23.804 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→75.2 Å
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Refine LS restraints |
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