[English] 日本語
Yorodumi
- PDB-1lk9: The Three-dimensional Structure of Alliinase from Garlic -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lk9
TitleThe Three-dimensional Structure of Alliinase from Garlic
ComponentsALLIIN LYASEAlliinase
KeywordsLYASE / EGF-like domain / PLP type 1 / chloride binding
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
2-AMINO-ACRYLIC ACID / PYRIDOXAL-5'-PHOSPHATE / Alliin lyase 1
Similarity search - Component
Biological speciesAllium sativum (garlic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.53 Å
AuthorsKuettner, E.B. / Hilgenfeld, R. / Weiss, M.S.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: The active principle of garlic at atomic resolution
Authors: Kuettner, E.B. / Hilgenfeld, R. / Weiss, M.S.
#1: Journal: Arch.Biochem.Biophys. / Year: 2002
Title: PURIFICATION, CHARACTERIZATION AND CRYSTALLIZATION OF ALLIINASE FROM GARLIC
Authors: KUETTNER, E.B. / HILGENFELD, R. / WEISS, M.S.
#2: Journal: Arch.Biochem.Biophys. / Year: 2002
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
DepositionApr 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
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 / diffrn_source / 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_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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 600heterogen 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 999sequence 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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ALLIIN LYASE
B: ALLIIN LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,16724
Polymers103,0332
Non-polymers4,13422
Water14,952830
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14250 Å2
ΔGint-168 kcal/mol
Surface area32330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.45, 101.07, 155.69
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein ALLIIN LYASE / Alliinase / ALLIINASE / CYSTEINE SULPHOXIDE LYASE


Mass: 51516.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: bulb / Source: (natural) Allium sativum (garlic) / References: UniProt: Q01594, alliin lyase

-
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


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
#3: 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.: 2
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
#4: 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

-
Non-polymers , 6 types, 848 molecules

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


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#8: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#9: Chemical ChemComp-DHA / 2-AMINO-ACRYLIC ACID / 2,3-DIDEHYDROALANINE / Dehydroalanine


Type: peptide linking / Mass: 87.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5NO2
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 830 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mMHEPES1reservoirpH7.4
210 %(v/v)glycerol1reservoir
320000 mMPLP1reservoir
43 mM1reservoirNaN3
55 mMprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 25, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
MLPHAREphasing
REFMAC4.0.6refinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.53→12 Å / SU B: 1.52975 / SU ML: 0.05519 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07531 / ESU R Free: 0.07692 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2207 3264 -RANDOM
Rwork0.1929 ---
all-162892 --
obs-162892 98.7 %-
Displacement parametersBiso mean: 25.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.53→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6862 0 252 830 7944
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_planar_d0.030.05
X-RAY DIFFRACTIONp_chiral_restr0.120.15
X-RAY DIFFRACTIONp_singtor_nbd0.1740.3
X-RAY DIFFRACTIONp_multtor_nbd0.190.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1250.3
X-RAY DIFFRACTIONp_planar_tor3.97
X-RAY DIFFRACTIONp_staggered_tor13.415
X-RAY DIFFRACTIONp_transverse_tor25.920
X-RAY DIFFRACTIONp_mcbond_it0.9411.5
X-RAY DIFFRACTIONp_mcangle_it1.3642.5
X-RAY DIFFRACTIONp_scbond_it3.3665
X-RAY DIFFRACTIONp_scangle_it4.60310
LS refinement shellResolution: 1.53→1.604 Å
RfactorNum. reflection% reflection
Rfree0.281 406 -
Rwork0.259 --
obs-20789 99.48 %
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.221 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.2

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more