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- PDB-1e6q: MYROSINASE FROM SINAPIS ALBA with the bound transition state anal... -

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Basic information

Entry
Database: PDB / ID: 1e6q
TitleMYROSINASE FROM SINAPIS ALBA with the bound transition state analogue gluco-tetrazole
ComponentsMYROSINASE MA1
KeywordsHYDROLASE / FAMILY 1 GLYCOSYL HYDROLASE / GLUCOSINOLATE / TIM BARREL / D-GLUCONO-1 / 5-LACTONE / TRANSITION STATE
Function / homology
Function and homology information


thioglucosidase / thioglucosidase activity / vacuole / beta-glucosidase activity / 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
NOJIRIMYCINE TETRAZOLE / Myrosinase MA1
Similarity search - Component
Biological speciesSINAPIS ALBA (white mustard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBurmeister, W.P.
Citation
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.
#1: Journal: Structure / Year: 1997
Title: The Crystal Structures of Sinapis Alba Myrosinase and a Covalent Glycosyl-Enzyme Intermediate Provide Insights Into the Substrate Recognition and Active-Site Machinery of an S-Glycosidase
Authors: Burmeister, W.P. / Cottaz, S. / Driguez, H. / Iori, R. / Palmieri, S. / Henrissat, B.
History
DepositionAug 22, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 5, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jan 21, 2015Group: Derived calculations
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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _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_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
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
M: MYROSINASE MA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,19223
Polymers57,0781
Non-polymers5,11422
Water14,196788
1
M: MYROSINASE MA1
hetero molecules

M: MYROSINASE MA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,38446
Polymers114,1572
Non-polymers10,22844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area16040 Å2
ΔGint-182.2 kcal/mol
Surface area38980 Å2
MethodPISA
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-1520-

ZN

21M-2026-

HOH

31M-2270-

HOH

41M-2292-

HOH

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Components

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Protein , 1 types, 1 molecules M

#1: Protein MYROSINASE MA1 / THIOGLUCOSIDE GLUCOHYDROLASE / SINIGRINASE / THIOGLUCOSIDASE


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

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Sugars , 4 types, 9 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.: 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
#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, 801 molecules

#6: Chemical ChemComp-NTZ / NOJIRIMYCINE TETRAZOLE


Mass: 202.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N4O4
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 788 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsACTIVE SITE NUCLEOPHILE: GLU409 AT THE POSITION OF THE GENERAL ACID/BASE: GLN187
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: 3.2 Å3/Da / Density % sol: 50 % / Description: ONLY THE LIGAND DIFFERS
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
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Details: Burmeister, W.P., (1997) Structure (London), 5, 663.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlmyrosinase1drop
230 mMHEPES1drop
30.05 %1dropNaN3
466 %satammonium sulfate1reservoir
5100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 1998 / Details: BENT MULTILAYER, SAGITALLY FOCUSING CRYSTAL
RadiationMonochromator: DIAMOND C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.35→17.5 Å / Num. obs: 151092 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 6.4
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 3 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.278 / % possible all: 94.9
Reflection shell
*PLUS
% possible obs: 94.9 %

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E4M

1e4m


Resolution: 1.35→10 Å / SU B: 0.45 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.039 / Details: ANISOTROPIC INDIVIDUAL B-FACTOR REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.146 7600 5 %RANDOM
Rwork0.119 ---
obs-150242 93.7 %-
Displacement parametersBiso mean: 16.2 Å2
Refinement stepCycle: LAST / Resolution: 1.35→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 324 788 5128
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.02
X-RAY DIFFRACTIONp_angle_d0.0360.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0420.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.52
X-RAY DIFFRACTIONp_mcangle_it3.33
X-RAY DIFFRACTIONp_scbond_it3.62
X-RAY DIFFRACTIONp_scangle_it4.43
X-RAY DIFFRACTIONp_plane_restr0.0080.02
X-RAY DIFFRACTIONp_chiral_restr0.1590.15
X-RAY DIFFRACTIONp_singtor_nbd0.1680.3
X-RAY DIFFRACTIONp_multtor_nbd0.2850.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1590.3
X-RAY DIFFRACTIONp_planar_tor9.67
X-RAY DIFFRACTIONp_staggered_tor11.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor26.220
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.119
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.35 Å / Lowest resolution: 1.42 Å / Rfactor Rfree: 0.196 / Rfactor obs: 0.154

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