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- PDB-1f7b: CRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1f7b | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEMOPHILUS INFLUENZAE: CRYSTAL FORM II IN COMPLEX WITH 4-OXO-SIALIC ACID | ||||||
![]() | N-ACETYL-NEURAMINATE LYASE | ||||||
![]() | LYASE / BETA BARREL | ||||||
Function / homology | ![]() N-acetylneuraminate lyase / N-acetylneuraminate lyase activity / N-acetylneuraminate catabolic process / carbohydrate metabolic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Barbosa, J.A.R.G. / Smith, B.J. / DeGori, R. / Lawrence, M.C. | ||||||
![]() | ![]() Title: Active site modulation in the N-acetylneuraminate lyase sub-family as revealed by the structure of the inhibitor-complexed Haemophilus influenzae enzyme. Authors: Barbosa, J.A.R.G. / Smith, B.J. / DeGori, R. / Ooi, H.C. / Marcuccio, S.M. / Campi, E.M. / Jackson, W.R. / Brossmer, R. / Sommer, M. / Lawrence, M.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.3 KB | Display | ![]() |
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PDB format | ![]() | 114.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 31.9 KB | Display | |
Data in CIF | ![]() | 49.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Details | The biological assembly is a tetramer constructed from chains A and C generated by the two-fold. |
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Components
#1: Protein | Mass: 32561.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NAU / | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-NAV / | #5: 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: 48.84 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, sodium acetate, ammonium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→15 Å / Num. all: 59168 / Num. obs: 52684 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.2 / Num. unique all: 5816 / % possible all: 42.4 |
Reflection | *PLUS Num. measured all: 231047 |
Reflection shell | *PLUS % possible obs: 42.4 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.2 |
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Processing
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Refinement | Resolution: 1.8→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor obs: 0.167 / Rfactor Rfree: 0.21 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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