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- PDB-2hor: Crystal structure of alliinase from garlic- apo form -

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Basic information

Entry
Database: PDB / ID: 2hor
TitleCrystal structure of alliinase from garlic- apo form
ComponentsAlliin lyase 1Alliinase
KeywordsLYASE / alliinase / garlic / Allium sativum / glycosylation / plant enzyme / Pyridoxal-5'-phosphate / aminoacrylate / apo form
Function / homology
Function and homology information


alliin lyase / alliin lyase activity / vacuole / chloride ion binding / 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 / Aspartate Aminotransferase; domain 2 ...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
ACETATE ION / NITRATE ION / Alliin lyase 1
Similarity search - Component
Biological speciesAllium sativum (garlic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 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 characterization
History
DepositionJul 16, 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: Derived calculations / Version format compliance
Revision 1.3Apr 16, 2014Group: Other
Revision 1.4Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
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_struct_special_symmetry / pdbx_validate_chiral / 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_struct_special_symmetry.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 999SEQUENCE 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

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Assembly

Deposited unit
A: Alliin lyase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,00712
Polymers49,0571
Non-polymers1,95011
Water8,935496
1
A: Alliin lyase 1
hetero molecules

A: Alliin lyase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,01424
Polymers98,1132
Non-polymers3,90122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area16890 Å2
ΔGint-197 kcal/mol
Surface area31170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)81.118, 81.118, 164.017
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-707-

NO3

21A-1162-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


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

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(2-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(2-3)-[alpha-D-mannopyranose-(1-6)]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: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa2-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Altp]{[(3+2)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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 , 5 types, 505 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 496 / Source method: isolated from a natural source / Formula: H2O

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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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Hampton Crystal screen condition number 39, 0.1M Hepes pH 7.5, 2% v/v PEG 400 and 2.0M ammonium sulfate. The crystals took between 4 to 6 months to appear and grew to a maximum size of 0.1 x ...Details: Hampton Crystal screen condition number 39, 0.1M Hepes pH 7.5, 2% v/v PEG 400 and 2.0M ammonium sulfate. The crystals took between 4 to 6 months to appear and grew to a maximum size of 0.1 x 0.1 x 0.1mm3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9737 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 16, 2004 / Details: double monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9737 Å / Relative weight: 1
ReflectionResolution: 1.6→42 Å / Num. all: 72527 / Num. obs: 72527 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.089 / Χ2: 1.35 / Net I/σ(I): 29.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3559 / Rsym value: 0.52 / Χ2: 0.769 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→39.6 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.677 / SU ML: 0.05 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0.52 / ESU R: 0.075 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.179 3663 5 %RANDOM
Rwork0.163 ---
all0.164 72527 --
obs0.164 72527 99.88 %-
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: 25.479 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2--0.65 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 120 496 4043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223743
X-RAY DIFFRACTIONr_bond_other_d0.0010.022550
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.985097
X-RAY DIFFRACTIONr_angle_other_deg0.8843.0036194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4155455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.40124.318176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23615636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6131519
X-RAY DIFFRACTIONr_chiral_restr0.0810.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024081
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02757
X-RAY DIFFRACTIONr_nbd_refined0.2030.2732
X-RAY DIFFRACTIONr_nbd_other0.1890.22663
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21843
X-RAY DIFFRACTIONr_nbtor_other0.0910.21832
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2340
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.2119
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.230
X-RAY DIFFRACTIONr_mcbond_it0.8011.52833
X-RAY DIFFRACTIONr_mcbond_other0.1641.5880
X-RAY DIFFRACTIONr_mcangle_it0.93823535
X-RAY DIFFRACTIONr_scbond_it1.91131865
X-RAY DIFFRACTIONr_scangle_it2.524.51548
LS refinement shellResolution: 1.6→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 254 -
Rwork0.22 5021 -
obs-5275 99.96 %

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