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Open data
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Basic information
Entry | Database: PDB / ID: 1lk9 | |||||||||
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Title | The Three-dimensional Structure of Alliinase from Garlic | |||||||||
![]() | ALLIIN LYASE | |||||||||
![]() | LYASE / EGF-like domain / PLP type 1 / chloride binding | |||||||||
Function / homology | ![]() alliin lyase / alliin lyase activity / amino acid metabolic process / vacuole / transaminase activity / chloride ion binding / pyridoxal phosphate binding / protein homodimerization activity Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kuettner, E.B. / Hilgenfeld, R. / Weiss, M.S. | |||||||||
![]() | ![]() Title: The active principle of garlic at atomic resolution Authors: Kuettner, E.B. / Hilgenfeld, R. / Weiss, M.S. #1: ![]() Title: PURIFICATION, CHARACTERIZATION AND CRYSTALLIZATION OF ALLIINASE FROM GARLIC Authors: KUETTNER, E.B. / HILGENFELD, R. / WEISS, M.S. #2: ![]() Title: Erratum to ``Purification, characterization and crystallization of alliinase from garlic. [Arch. Biochem. Biophys. 402, 192-200.]'' Authors: Kuettner, E.B. / Hilgenfeld, R. / Weiss, M.S. | |||||||||
History |
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Remark 600 | heterogen The molecules EPE and DHA are only present at an occupancy of 50%. Their presence is ...heterogen The molecules EPE and DHA are only present at an occupancy of 50%. Their presence is mutually exclusive. | |||||||||
Remark 999 | sequence there are two different sequences in the literature, one contains an Asp in position 176 ...sequence there are two different sequences in the literature, one contains an Asp in position 176 and one contains Asn. The authors have built and refined the structure with an Asp present in this position. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 204.1 KB | Display | ![]() |
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PDB format | ![]() | 165.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 43 KB | Display | |
Data in CIF | ![]() | 64.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 51516.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: bulb / Source: (natural) ![]() ![]() |
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-Sugars , 3 types, 4 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
-Non-polymers , 6 types, 848 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/DHA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/DHA.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-DHA / | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.6 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PROTEIN: 5 MG/ML ALLIINASE, 5 MM HEPES PH 7.4, 10 % (V/V) GLYCEROL, 0.25 MM PYRIDOXAL-5'-PHOSPHATE, 1 MM S-ETHYL-L-CYSTEINE; PRECIPITANT: 2.9 M AMMONIUM SULFATE, 50 MM HEPES PH 7.4 HANGING ...Details: PROTEIN: 5 MG/ML ALLIINASE, 5 MM HEPES PH 7.4, 10 % (V/V) GLYCEROL, 0.25 MM PYRIDOXAL-5'-PHOSPHATE, 1 MM S-ETHYL-L-CYSTEINE; PRECIPITANT: 2.9 M AMMONIUM SULFATE, 50 MM HEPES PH 7.4 HANGING DROP METHOD(4 MICROL + 4 MICROL), VAPOUR DIFFUSION, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃Details: Kuettner, E.B., (2002) Arch.Biochem.Biophys., 402, 192. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 25, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8423 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→12 Å / Num. all: 160747 / Num. obs: 160747 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.53→1.56 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8024 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 928820 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 99.6 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 25.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.53→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.53→1.604 Å
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.221 / Rfactor Rwork: 0.193 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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