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- PDB-6sxt: GH54 a-l-arabinofuranosidase soaked with aziridine inhibitor -

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Basic information

Entry
Database: PDB / ID: 6sxt
TitleGH54 a-l-arabinofuranosidase soaked with aziridine inhibitor
ComponentsAlpha-L-arabinofuranosidase B
KeywordsHYDROLASE / Covalent complex / Arabinofuranosidase / GH54 / Aspergillus
Function / homology
Function and homology information


arabinose metabolic process / arabinan catabolic process / L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / xylan catabolic process / extracellular region
Similarity search - Function
Alpha-L-arabinofuranosidase B, catalytic / Alpha-L-arabinofuranosidase B / Alpha-L-arabinofuranosidase B, catalytic / Alpha-L-arabinofuranosidase B, arabinose-binding domain / Alpha-L-arabinofuranosidase B, arabinose-binding domain superfamily / Alpha-L-arabinofuranosidase B (ABFB) domain / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls - #200 ...Alpha-L-arabinofuranosidase B, catalytic / Alpha-L-arabinofuranosidase B / Alpha-L-arabinofuranosidase B, catalytic / Alpha-L-arabinofuranosidase B, arabinose-binding domain / Alpha-L-arabinofuranosidase B, arabinose-binding domain superfamily / Alpha-L-arabinofuranosidase B (ABFB) domain / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / ALANINE / Chem-LXE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Alpha-L-arabinofuranosidase B
Similarity search - Component
Biological speciesAspergillus kawachii (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.466 Å
AuthorsMcGregor, N.G.S. / Davies, G.J. / Nin-Hill, A. / Rovira, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/R001162/1 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Rational Design of Mechanism-Based Inhibitors and Activity-Based Probes for the Identification of Retaining alpha-l-Arabinofuranosidases.
Authors: McGregor, N.G.S. / Artola, M. / Nin-Hill, A. / Linzel, D. / Haon, M. / Reijngoud, J. / Ram, A. / Rosso, M.N. / van der Marel, G.A. / Codee, J.D.C. / van Wezel, G.P. / Berrin, J.G. / Rovira, ...Authors: McGregor, N.G.S. / Artola, M. / Nin-Hill, A. / Linzel, D. / Haon, M. / Reijngoud, J. / Ram, A. / Rosso, M.N. / van der Marel, G.A. / Codee, J.D.C. / van Wezel, G.P. / Berrin, J.G. / Rovira, C. / Overkleeft, H.S. / Davies, G.J.
History
DepositionSep 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_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 / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn
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.occupancy / _atom_site.type_symbol / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.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_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_type / chem_comp ...atom_type / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-L-arabinofuranosidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,32032
Polymers50,9711
Non-polymers3,34931
Water8,215456
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint28 kcal/mol
Surface area17420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.232, 112.232, 342.730
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-505-

SO4

21A-505-

SO4

31A-512-

SO4

41A-601-

HOH

51A-880-

HOH

61A-883-

HOH

71A-991-

HOH

81A-1055-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-L-arabinofuranosidase B / Arabinosidase B


Mass: 50970.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus kawachii (strain NBRC 4308) (mold)
Strain: NBRC 4308 / Gene: abfB, AKAW_08685 / Plasmid: pPICZa / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33
References: UniProt: Q8NK89, non-reducing end alpha-L-arabinofuranosidase

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Sugars , 2 types, 2 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
#4: 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.: 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 , 8 types, 485 molecules

#3: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-LXE / [(1~{S},2~{S},3~{S},4~{S})-2-(hydroxymethyl)-3,4-bis(oxidanyl)cyclopentyl]azanium


Mass: 148.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14NO3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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 % sol: 34 %
Description: Triangular prisms roughly twice as long as the triangle face is tall.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 2:1 protein:well solution. 0.1 M pH 4.5 sodium acetate buffer, 60% PEG400, 0.3 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 1, 2019
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.466→85.54 Å / Num. obs: 141273 / % possible obs: 99.3 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.031 / Rrim(I) all: 0.109 / Net I/σ(I): 13
Reflection shellResolution: 1.466→1.491 Å / Redundancy: 10.7 % / Rmerge(I) obs: 2.98 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 6968 / CC1/2: 0.367 / Rpim(I) all: 0.94 / Rrim(I) all: 3.13 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSMar 15, 2019data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WD3

1wd3


Resolution: 1.466→84.687 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / Cross valid method: FREE R-VALUE / ESU R: 0.045 / ESU R Free: 0.048
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1791 6980 4.941 %
Rwork0.1569 --
all0.158 --
obs-141273 99.26 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.664 Å2
Baniso -1Baniso -2Baniso -3
1-0.154 Å20.077 Å2-0 Å2
2--0.154 Å2-0 Å2
3----0.499 Å2
Refinement stepCycle: LAST / Resolution: 1.466→84.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3578 0 207 456 4241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0133897
X-RAY DIFFRACTIONr_bond_other_d0.0370.0173292
X-RAY DIFFRACTIONr_angle_refined_deg1.9421.6715282
X-RAY DIFFRACTIONr_angle_other_deg2.5771.5887675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5675497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.43924.054185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.5815508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0621512
X-RAY DIFFRACTIONr_chiral_restr0.0970.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024426
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02799
X-RAY DIFFRACTIONr_nbd_refined0.2190.2718
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2220.23221
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21927
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.21752
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2349
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4110.234
X-RAY DIFFRACTIONr_nbd_other0.3890.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2210.230
X-RAY DIFFRACTIONr_mcbond_it1.7371.9691951
X-RAY DIFFRACTIONr_mcbond_other1.6961.9651948
X-RAY DIFFRACTIONr_mcangle_it2.2412.9392438
X-RAY DIFFRACTIONr_mcangle_other2.2412.9422439
X-RAY DIFFRACTIONr_scbond_it3.1952.3231946
X-RAY DIFFRACTIONr_scbond_other3.1942.3251947
X-RAY DIFFRACTIONr_scangle_it4.33.3292836
X-RAY DIFFRACTIONr_scangle_other4.2993.3312837
X-RAY DIFFRACTIONr_lrange_it5.34425.3834377
X-RAY DIFFRACTIONr_lrange_other5.07424.7644280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.466-1.5040.314730.2989804X-RAY DIFFRACTION98.063
1.504-1.5450.284920.2799506X-RAY DIFFRACTION98.5899
1.545-1.590.2814950.2569253X-RAY DIFFRACTION98.7639
1.59-1.6390.2474990.2369014X-RAY DIFFRACTION98.8877
1.639-1.6920.2134890.2118751X-RAY DIFFRACTION99.0248
1.692-1.7520.2344800.198508X-RAY DIFFRACTION99.1287
1.752-1.8180.1864150.1738205X-RAY DIFFRACTION99.2744
1.818-1.8920.1914100.1617940X-RAY DIFFRACTION99.3929
1.892-1.9760.1674030.1457594X-RAY DIFFRACTION99.4775
1.976-2.0730.1473640.1387342X-RAY DIFFRACTION99.6251
2.073-2.1850.1513340.1336972X-RAY DIFFRACTION99.6726
2.185-2.3170.1553150.1316638X-RAY DIFFRACTION99.7704
2.317-2.4770.1642960.1276259X-RAY DIFFRACTION99.7717
2.477-2.6750.1493140.1245780X-RAY DIFFRACTION99.918
2.675-2.9310.1732900.145345X-RAY DIFFRACTION99.9645
2.931-3.2760.1632610.1474848X-RAY DIFFRACTION99.9804
3.276-3.7830.1592190.1514315X-RAY DIFFRACTION99.9559
3.783-4.6310.1371880.1223686X-RAY DIFFRACTION100
4.631-6.5440.191470.1642882X-RAY DIFFRACTION100
6.544-84.6870.284960.2291653X-RAY DIFFRACTION98.9813

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