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- PDB-2hox: alliinase from allium sativum (garlic) -

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Basic information

Entry
Database: PDB / ID: 2hox
Titlealliinase from allium sativum (garlic)
ComponentsAlliin lyase 1
KeywordsLYASE / CYSTEINE SULPHOXIDE LYASE / ALLIINASE
Function / homology
Function and homology information


alliin lyase / alliin lyase activity / vacuole / amino acid metabolic process / chloride ion binding / transaminase activity / pyridoxal phosphate binding / protein homodimerization activity
Similarity search - Function
EGF-like, alliinase / Alliinase, EGF-like domain / Alliinase EGF-like domain / Alliinase, C-terminal / Alliinase, N-terminal domain superfamily / Allinase / : / Laminin / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 ...EGF-like, alliinase / Alliinase, EGF-like domain / Alliinase EGF-like domain / Alliinase, C-terminal / Alliinase, N-terminal domain superfamily / Allinase / : / Laminin / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / EGF-like domain signature 1. / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Ribbon / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-P1T / Alliin lyase 1
Similarity search - Component
Biological speciesAllium sativum (garlic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsShimon, L.J.W. / Rabinkov, A. / Wilcheck, M. / Mirelman, D. / Frolow, F.
Citation
Journal: J.Mol.Biol. / Year: 2007
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: Journal: Acta Crystallogr.,Sect.D / Year: 2002
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
DepositionJul 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 16, 2014Group: Other
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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 viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alliin lyase 1
B: Alliin lyase 1
C: Alliin lyase 1
D: Alliin lyase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,53325
Polymers196,2274
Non-polymers6,30621
Water48,0822669
1
A: Alliin lyase 1
B: Alliin lyase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,54214
Polymers98,1132
Non-polymers3,42912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12110 Å2
ΔGint-33 kcal/mol
Surface area33320 Å2
MethodPISA
2
C: Alliin lyase 1
D: Alliin lyase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,99111
Polymers98,1132
Non-polymers2,8779
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13540 Å2
ΔGint-43 kcal/mol
Surface area32870 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29170 Å2
ΔGint-85 kcal/mol
Surface area62670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.665, 126.892, 102.664
Angle α, β, γ (deg.)90.00, 97.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Alliin lyase 1 / Alliinase 1 / Cysteine sulphoxide lyase 1


Mass: 49056.625 Da / Num. of mol.: 4 / Fragment: ALLIIN lyase 1 / Source method: isolated from a natural source / Source: (natural) Allium sativum (garlic) / Tissue: BULBS / References: UniProt: Q01594, alliin lyase

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Sugars , 6 types, 13 molecules

#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


Type: oligosaccharide / Mass: 1026.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-2[DManpb1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a212h-1b_1-5]/1-2-1-3-4-3/a3-b1_a4-c1_c4-d1_d2-e1_d3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][b-D-Xylp]{}[(3+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#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


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3/a3-b1_a4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#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


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 2677 molecules

#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#9: Chemical
ChemComp-P1T / 2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID


Mass: 318.220 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H15N2O7P
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2669 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9333 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2003
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.93331
20.9331
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0013refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LK9

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
RfactorNum. reflection% reflectionSelection details
Rfree0.20452 16535 5.1 %RANDOM
Rwork0.16724 ---
obs0.16914 310776 96.47 %-
all-327315 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.133 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.44 Å2
2---0.45 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.4→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13748 0 408 2669 16825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02214576
X-RAY DIFFRACTIONr_bond_other_d0.0020.029951
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.97519777
X-RAY DIFFRACTIONr_angle_other_deg0.9913.00324079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11351708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.80824.168679
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.538152444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3171574
X-RAY DIFFRACTIONr_chiral_restr0.1090.22123
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215861
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022981
X-RAY DIFFRACTIONr_nbd_refined0.2210.22934
X-RAY DIFFRACTIONr_nbd_other0.20.210920
X-RAY DIFFRACTIONr_nbtor_refined0.1890.27287
X-RAY DIFFRACTIONr_nbtor_other0.0930.27220
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.21956
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.283
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.554310909
X-RAY DIFFRACTIONr_mcbond_other0.52933445
X-RAY DIFFRACTIONr_mcangle_it2.86513797
X-RAY DIFFRACTIONr_scbond_it4.54277238
X-RAY DIFFRACTIONr_scangle_it5.987105977
X-RAY DIFFRACTIONr_rigid_bond_restr6.646330843
X-RAY DIFFRACTIONr_sphericity_free25.39332178
X-RAY DIFFRACTIONr_sphericity_bonded10.818324090
LS refinement shellResolution: 1.4→1.432 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 960 -
Rwork0.309 17361 -
obs--73.6 %

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