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- PDB-1w9d: S. alba myrosinase in complex with S-ethyl phenylacetothiohydroxi... -

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Basic information

Entry
Database: PDB / ID: 1w9d
TitleS. alba myrosinase in complex with S-ethyl phenylacetothiohydroximate- O-sulfate
ComponentsGLYCOSIDASE
KeywordsHYDROLASE / THIOGLUCOSIDASE / THIOGLYCOSIDASE / MYROSINASE / THIO-GLUCOSIDE / THIOHYDROXIMATE / GLUSOSINOLATE / GLUCOTROPAEOLIN
Function / homology
Function and homology information


thioglucosidase / thioglucosidase activity / glucosinolate glucohydrolase activity / glucosinolate catabolic process / vacuole / beta-glucosidase activity / response to salt stress / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
S-BENZYL PHENYLACETOTHIOHYDROXIMATE-O-SULFATE / Myrosinase MA1
Similarity search - Component
Biological speciesSINAPIS ALBA (white mustard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBourderioux, A. / Lefoix, M. / Gueyrard, D. / Tatibouet, A. / Cottaz, S. / Arzt, S. / Burmeister, W.P. / Rollin, P.
Citation
Journal: Org.Biomol.Chem. / Year: 2005
Title: The Glucosinolate-Myrosinase System. New Insights Into Enzyme-Substrate Interactions by Use of Simplified Inhibitors
Authors: Bourderioux, A. / Lefoix, M. / Gueyrard, D. / Tatibouet, A. / Cottaz, S. / Arzt, S. / Burmeister, W.P. / Rollin, P.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: High Resolution X-Ray Crystallography Shows that Ascorbate is a Cofactor for Myrosinase and Substitutes for the Function of the Catalytic Base
Authors: Burmeister, W.P. / Cottaz, S. / Rollin, P. / Vasella, A. / Henrissat, B.
History
DepositionOct 8, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_conn_angle / pdbx_struct_special_symmetry / 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_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: GLYCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,31020
Polymers57,0781
Non-polymers5,23119
Water13,709761
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)135.300, 137.200, 80.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11M-1502-

ZN

21M-2026-

HOH

31M-2267-

HOH

41M-2294-

HOH

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Components

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Protein , 1 types, 1 molecules M

#1: Protein GLYCOSIDASE / MYROSINASE


Mass: 57078.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SINAPIS ALBA (white mustard) / Organ: SEED / Strain: EMERGO / Tissue: MYROSIN GRAINS / References: UniProt: P29736*PLUS, EC: 3.2.3.1

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Sugars , 4 types, 10 molecules

#2: 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
#3: Polysaccharide beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)- ...beta-D-xylopyranose-(1-2)-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: 864.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-2DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[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/a3-b1_a4-c1_c4-d1_d2-e1WURCSPDB2Glycan 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]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D- ...beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][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: 1189.079 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-2[DManpa1-3][DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a212h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-5-5/a3-b1_a4-c1_c4-d1_d2-e1_d3-f1_d6-g1WURCSPDB2Glycan 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)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: 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.: 6
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, 770 molecules

#6: Chemical ChemComp-SEH / S-BENZYL PHENYLACETOTHIOHYDROXIMATE-O-SULFATE / ETHYL (1E)-2-PHENYL-N-(SULFOOXY)ETHANIMIDOTHIOATE


Mass: 275.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13NO4S2
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 761 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsOUR SEQUENCE IS AN X-RAY SEQUENCE BASED ON THE ASSIGNMENT OF THE RESIDUES BY THEIR ELECTRON DENSITY. ...OUR SEQUENCE IS AN X-RAY SEQUENCE BASED ON THE ASSIGNMENT OF THE RESIDUES BY THEIR ELECTRON DENSITY. SOME AMBIGUITIES MAY EXIST. FURTHERMORE A DIFFERENT ISOFORM OF THE ENZYME MAY BE PRESENT IN THE CRYSTAL. THE SEQUENCE WAS ORIGINALLY IDENTIFIED DURING THE DETERMINATION OF THE STRUCTURE IN PDB ENTRY 1E4M.

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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: 3.2 Å3/Da / Density % sol: 50 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: HANGING DROP METHOD, 12 MG/ML PROTEIN IN 30 MM HEPES, PH 6.5, 0.05 % NAN3, PRECIPITANT 66% SAT. AMMONIUM SULFATE, 100MM TRIS-HCL PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 27, 2002 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND 111 AND SI220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.4→35 Å / Num. obs: 146755 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 6.1
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.4 / % possible all: 97.4

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E4M

1e4m


Resolution: 1.6→35 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: INHIBITOR TOPOLOGY AND PARAMETERS SAME AS IN ENTRY 1W9B, ONLY MOST OF THE ATOMS OF THE GLUCOSE GROUP HAVE BEEN DELETED. THE INHIBITOR HAS BEEN RENAMED FROM CGT TO SEH AFTER REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.195 7192 4.9 %RANDOM
Rwork0.1886 ---
obs0.1886 97986 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.9271 Å2 / ksol: 0.380436 e/Å3
Displacement parametersBiso mean: 18.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.995 Å20 Å20 Å2
2---0.433 Å20 Å2
3----0.562 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.6→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 335 761 5112
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012469
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.79857
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.82
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.482.5
X-RAY DIFFRACTIONc_mcangle_it2.423
X-RAY DIFFRACTIONc_scbond_it2.163
X-RAY DIFFRACTIONc_scangle_it3.513.5
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.21 452 4.6 %
Rwork0.212 9252 -
obs--98.85 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CGT_PAR.TXT.PARCGT_TOP.TXT.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAMCARBOHYDRATE.TOP

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