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Open data
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Basic information
Entry | Database: PDB / ID: 3lcx | ||||||
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Title | L-KDO aldolase | ||||||
![]() | N-acetylneuraminate lyase | ||||||
![]() | LYASE / Tim barrel / Carbohydrate metabolism / 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 | ![]() ![]() ![]() | ||||||
![]() | Chou, C.-Y. / Huang, K.-F. / Wang, A.H.-J. / Ko, T.-P. | ||||||
![]() | ![]() Title: Modulation of substrate specificities of D-sialic acid aldolase through single mutations of Val251 Authors: Chou, C.-Y. / Ko, T.-P. / Wu, K.-J. / Huang, K.-F. / Lin, C.-H. / Wong, C.-H. / Wang, A.H.-J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 251.3 KB | Display | ![]() |
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PDB format | ![]() | 199.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3lbcC ![]() 3lbmC ![]() 3lcfC ![]() 3lcgC ![]() 3lchC ![]() 3lciC ![]() 3lclC ![]() 3lcwC ![]() 1nalS S: Starting model for refinement 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: 35133.270 Da / Num. of mol.: 4 Mutation: E60A, Y98H, F115L, D150G, N153Y, V251I, V265I, Y281C, L282Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2.0M ammonium sulfate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2007 / Details: vertically focusing mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99997 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→30 Å / Num. all: 115631 / Num. obs: 114937 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 45.3 |
Reflection shell | Highest resolution: 1.98 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 3.1 / Num. unique all: 11479 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB enrty 1NAL Resolution: 1.98→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 104 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.971 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.98→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.05 Å / Rfactor Rfree error: 0.0407
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Xplor file |
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