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- PDB-6sxr: E221Q mutant of GH54 a-l-arabinofuranosidase soaked with 4-nitrop... -

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Basic information

Entry
Database: PDB / ID: 6sxr
TitleE221Q mutant of GH54 a-l-arabinofuranosidase soaked with 4-nitrophenyl a-l-arabinofuranoside
ComponentsAlpha-L-arabinofuranosidase B
KeywordsHYDROLASE / Michaelis 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 / pectin catabolic process / 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 / 4-nitrophenyl alpha-L-arabinofuranoside / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Alpha-L-arabinofuranosidase B
Similarity search - Component
Biological speciesAspergillus kawachii IFO 4308 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _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.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
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,03135
Polymers50,8831
Non-polymers4,14834
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint37 kcal/mol
Surface area17150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.970, 111.970, 341.390
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-517-

PEG

21A-750-

HOH

31A-929-

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: 50882.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus kawachii IFO 4308 (mold) / Gene: abfB, AKAW_08685 / Plasmid: pPICZa / Production host: Komagataella pastoris (fungus)
References: UniProt: Q8NK89, non-reducing end alpha-L-arabinofuranosidase

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Sugars , 3 types, 5 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: 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
#6: Sugar ChemComp-KHP / 4-nitrophenyl alpha-L-arabinofuranoside / 2-HYDROXYMETHYL-5-(4-NITRO-PHENOXY)-TETRAHYDRO-FURAN-3,4-DIOL / 4-NITROPHENYL-ARA / 4-nitrophenyl alpha-L-arabinoside / 4-nitrophenyl L-arabinoside / 4-nitrophenyl arabinoside


Type: L-saccharide / Mass: 271.223 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H13NO7 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
4-nitrophenyl-AraIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 7 types, 381 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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 % 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, 0.4 M Li2SO4

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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 19, 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: 1.64→93.28 Å / Num. obs: 99211 / % possible obs: 98.2 % / Redundancy: 12.6 % / CC1/2: 1 / Rrim(I) all: 0.129 / Net I/σ(I): 12.5
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4864 / CC1/2: 0.5 / Rrim(I) all: 2.319 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
xia20.5.898data reduction
DIALS1.14.9data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WD3

1wd3


Resolution: 1.64→93.28 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / Cross valid method: FREE R-VALUE / ESU R: 0.062 / ESU R Free: 0.064
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.181 5141 5.182 %Random selection
Rwork0.1596 ---
all0.161 ---
obs-99210 98.143 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.156 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20.22 Å2-0 Å2
2--0.44 Å2-0 Å2
3----1.427 Å2
Refinement stepCycle: LAST / Resolution: 1.64→93.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3572 0 260 352 4184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133896
X-RAY DIFFRACTIONr_bond_other_d0.0370.0173273
X-RAY DIFFRACTIONr_angle_refined_deg1.8731.6965256
X-RAY DIFFRACTIONr_angle_other_deg2.5381.6127621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5625480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.40224.044183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.7315498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7651512
X-RAY DIFFRACTIONr_chiral_restr0.0860.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024380
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02797
X-RAY DIFFRACTIONr_nbd_refined0.2060.2698
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.23144
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21912
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21670
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2283
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3060.213
X-RAY DIFFRACTIONr_nbd_other0.1930.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.5010.219
X-RAY DIFFRACTIONr_mcbond_it2.0132.5451925
X-RAY DIFFRACTIONr_mcbond_other1.9352.5421922
X-RAY DIFFRACTIONr_mcangle_it2.4873.8052402
X-RAY DIFFRACTIONr_mcangle_other2.4913.8062403
X-RAY DIFFRACTIONr_scbond_it3.3963.0081971
X-RAY DIFFRACTIONr_scbond_other3.3623.0011968
X-RAY DIFFRACTIONr_scangle_it4.8224.3142853
X-RAY DIFFRACTIONr_scangle_other4.7544.3022848
X-RAY DIFFRACTIONr_lrange_it5.4532.0014256
X-RAY DIFFRACTIONr_lrange_other5.34931.6514201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.6830.3053760.2986814X-RAY DIFFRACTION96.835
1.683-1.7290.2943650.2736624X-RAY DIFFRACTION97.1234
1.729-1.7790.2533410.2476499X-RAY DIFFRACTION97.325
1.779-1.8330.2443320.2346337X-RAY DIFFRACTION97.5856
1.833-1.8940.2213430.2026117X-RAY DIFFRACTION97.6716
1.894-1.960.2013380.1845941X-RAY DIFFRACTION97.8647
1.96-2.0340.1812990.1615762X-RAY DIFFRACTION98.011
2.034-2.1170.1662770.1495563X-RAY DIFFRACTION98.2338
2.117-2.2110.1873170.1425311X-RAY DIFFRACTION98.34
2.211-2.3190.1752740.1385118X-RAY DIFFRACTION98.556
2.319-2.4440.1642620.1344877X-RAY DIFFRACTION98.486
2.444-2.5930.1762530.1334629X-RAY DIFFRACTION98.8259
2.593-2.7720.1852400.1394365X-RAY DIFFRACTION99.011
2.772-2.9930.1892150.1494088X-RAY DIFFRACTION99.1246
2.993-3.2790.1782170.1543774X-RAY DIFFRACTION99.2786
3.279-3.6660.1722130.1573404X-RAY DIFFRACTION99.3954
3.666-4.2320.141770.143037X-RAY DIFFRACTION99.4123
4.232-5.1810.1441300.1242603X-RAY DIFFRACTION99.3818
5.181-7.320.1641120.1712028X-RAY DIFFRACTION99.0741
7.32-93.280.235600.2141178X-RAY DIFFRACTION97.2506

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