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- PDB-1fdz: N-ACETYLNEURAMINATE LYASE IN COMPLEX WITH PYRUVATE VIA BOROHYDRID... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fdz | |||||||||
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Title | N-ACETYLNEURAMINATE LYASE IN COMPLEX WITH PYRUVATE VIA BOROHYDRIDE REDUCTION | |||||||||
![]() | N-ACETYLNEURAMINATE LYASE | |||||||||
![]() | LYASE / ALDOLASE / OXO-ACID LYASE / ALPHA-KETO-ACID LYASE / CARBON-CARBON LYASE | |||||||||
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 | ![]() ![]() | |||||||||
![]() | Lawrence, M.C. / Barbosa, J.A.R.G. / Smith, B.J. / Hall, N.E. / Pilling, P.A. / Ooi, H.C. / Marcuccio, S.M. | |||||||||
![]() | ![]() Title: Structure and mechanism of a sub-family of enzymes related to N-acetylneuraminate lyase. Authors: Lawrence, M.C. / Barbosa, J.A.R.G. / Smith, B.J. / Hall, N.E. / Pilling, P.A. / Ooi, H.C. / Marcuccio, S.M. #1: ![]() Title: The Three-Dimensional Structure of N-Acetylneuraminate Lyase from Escherichia Coli Authors: Izard, T. / Lawrence, M.C. / Malby, R.L. / Lilley, G.G. / Colman, P.M. #2: ![]() Title: High-Level Production and Purification of Escherichia Coli N-Acetylneuraminic Acid Aldolase (Ec 4.1.3.3) Authors: Lilley, G.G. / Von Itzstein, M. / Ivanecic, N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 233.9 KB | Display | ![]() |
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PDB format | ![]() | 188.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.3 KB | Display | ![]() |
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Full document | ![]() | 500.2 KB | Display | |
Data in XML | ![]() | 46.5 KB | Display | |
Data in CIF | ![]() | 64.2 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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Unit cell |
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Components
#1: Protein | Mass: 32626.375 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: COVALENT COMPLEX, OBTAINED BY REDUCTION WITH BOROHYDRIDE FROM AN ENZYME - SIALIC ACID MIX Source: (gene. exp.) ![]() ![]() Description: DESCRIBED IN LILLEY, G.G. ET AL. (1992) SEE REFERENCE BELOW; OBTAINED BY BOROHYDRIDE REDUCTION OF ENZYME IN COMPLEX WITH SIALIC ACID Gene: NPL / Production host: ![]() ![]() #2: Chemical | ChemComp-PYR / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 56 % | |||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.9 Details: HANGING DROP VAPOR DIFFUSION. WELL: 53% SATURATED AMMONIUM SULFATE, 75 MILLIMOLAR SODIUM PHOSPHATE BUFFER (PH 6.9). DROP: EQUAL VOLUMES OF WELL AND PRE-REACTED ENZYME, SIALIC ACID AND ...Details: HANGING DROP VAPOR DIFFUSION. WELL: 53% SATURATED AMMONIUM SULFATE, 75 MILLIMOLAR SODIUM PHOSPHATE BUFFER (PH 6.9). DROP: EQUAL VOLUMES OF WELL AND PRE-REACTED ENZYME, SIALIC ACID AND BOROHYDRIDE MIX (SEE JRNL), vapor diffusion - hanging drop | |||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.2 / Method: microdialysis | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 1, 1995 / Details: MSC MIRROR SYSTEM |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→15 Å / Num. obs: 49914 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.67 / % possible all: 84.3 |
Reflection | *PLUS Num. measured all: 203660 |
Reflection shell | *PLUS % possible obs: 74 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FDZ (ENZYME-3-HYDROXYPYRUVATE COMPLEX) Resolution: 2.6→6 Å / σ(F): 0
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Displacement parameters | Biso mean: 27.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→6 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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