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Open data
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Basic information
Entry | Database: PDB / ID: 2hox | |||||||||
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Title | alliinase from allium sativum (garlic) | |||||||||
![]() | Alliin lyase 1![]() | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Shimon, L.J.W. / Rabinkov, A. / Wilcheck, M. / Mirelman, D. / Frolow, F. | |||||||||
![]() | ![]() Title: Two Structures of Alliinase from Alliium sativum L.: Apo Form and Ternary Complex with Aminoacrylate Reaction Intermediate Covalently Bound to the PLP Cofactor. Authors: Shimon, L.J. / Rabinkov, A. / Shin, I. / Miron, T. / Mirelman, D. / Wilchek, M. / Frolow, F. #1: ![]() Title: Alliin Lyase (Alliinase from Garlic (Allium Sativum) Crystallization and Preliminary X-Ray Characterization Authors: Shimon, L.J.W. / Rabinkov, A. / Miron, T. / Mirelman, D. / Wilcheck, M. / Frolow, F. | |||||||||
History |
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Remark 999 | SEQUENCE THERE IS A VARIATION IN A SEQUENCE ASSIGNEMENT IN THE LITERATURE,ONE CONTAINS AN ASP IN ... SEQUENCE THERE IS A VARIATION IN A SEQUENCE ASSIGNEMENT 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 IN ACCORD WITH THE RELATED STRUCTURE 1LK9. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 424 KB | Display | ![]() |
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PDB format | ![]() | 339.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2horC ![]() 1lk9S C: citing same article ( 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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2 | ![]()
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3 |
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | ![]() Mass: 49056.625 Da / Num. of mol.: 4 / Fragment: ALLIIN lyase 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() ![]() |
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-Sugars , 6 types, 13 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | beta-D-xylopyranose-(1-2)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-xylopyranose-(1-2)-[beta-D-mannopyranose-(1-3)]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 | alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source |
#4: 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 |
#5: Polysaccharide | alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source |
#6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source |
#7: Sugar | ChemComp-NAG / ![]() |
-Non-polymers , 3 types, 2677 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/P1T.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/P1T.gif)
![](data/chem/img/HOH.gif)
#8: Chemical | ChemComp-CL / ![]() #9: Chemical | ChemComp-P1T / #10: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.7 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 4000, AMMONIUM ACETATE, TRI- SODIUM CITRATE, PH 5.6, pH 5.60, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2003 | |||||||||
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.39→46.1 Å / Num. all: 327315 / Num. obs: 327315 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.08 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 40.4 | |||||||||
Reflection shell | Resolution: 1.39→1.41 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.598 / % possible all: 78.1 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1LK9 Resolution: 1.4→46.1 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.305 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.068 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.133 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→46.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.432 Å / Total num. of bins used: 20
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