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- PDB-6sxv: GH51 a-l-arabinofuranosidase soaked with aziridine inhibitor -

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Basic information

Entry
Database: PDB / ID: 6sxv
TitleGH51 a-l-arabinofuranosidase soaked with aziridine inhibitor
ComponentsGH51 a-l-arabinofuranosidase
KeywordsHYDROLASE / Covalent complex / Arabinofuranosidase / GH51 / Geobacillus
Function / homology
Function and homology information


arabinan catabolic process / L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / cytoplasm
Similarity search - Function
Alpha-L-arabinofuranosidase, C-terminal / Alpha-L-arabinofuranosidase C-terminal domain / Alpha-L-arabinofuranosidase C-terminus / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like ...Alpha-L-arabinofuranosidase, C-terminal / Alpha-L-arabinofuranosidase C-terminal domain / Alpha-L-arabinofuranosidase C-terminus / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-ETE / Chem-LXE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.402 Å
AuthorsMcGregor, N.G.S. / Davies, G.J.
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 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / 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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 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: GH51 a-l-arabinofuranosidase
B: GH51 a-l-arabinofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,26617
Polymers114,5702
Non-polymers1,69615
Water15,475859
1
A: GH51 a-l-arabinofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1509
Polymers57,2851
Non-polymers8658
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GH51 a-l-arabinofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1168
Polymers57,2851
Non-polymers8317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)178.994, 178.994, 100.893
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein GH51 a-l-arabinofuranosidase


Mass: 57284.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: AbfA / Plasmid: pET28-NHisTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold
References: UniProt: Q9XBQ3, non-reducing end alpha-L-arabinofuranosidase

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Non-polymers , 6 types, 874 molecules

#2: 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.: 2 / Source method: obtained synthetically / Formula: C6H14NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O5
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 859 / 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 Matthews: 2.73 Å3/Da / Density % sol: 54.92 % / Description: Rhombohedral
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2:1 protein:well solution. 0.1 M pH 7.5 Tris-HCl buffer, 18% PEG3350, 0.7 M NH4F, 5% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 18, 2018
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.4→29.85 Å / Num. obs: 235421 / % possible obs: 99.5 % / Redundancy: 6.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Net I/σ(I): 10.8
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 16547 / CC1/2: 0.78 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSAug. 8, 2018data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PZ3

1pz3


Resolution: 1.402→29.85 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.97 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.051
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1784 12425 5.278 %
Rwork0.1702 --
all0.171 --
obs-235420 99.512 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.467 Å2
Baniso -1Baniso -2Baniso -3
1-0.055 Å20.027 Å20 Å2
2--0.055 Å20 Å2
3----0.177 Å2
Refinement stepCycle: LAST / Resolution: 1.402→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7747 0 110 859 8716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0138288
X-RAY DIFFRACTIONr_bond_other_d0.0350.0177475
X-RAY DIFFRACTIONr_angle_refined_deg2.1691.6411320
X-RAY DIFFRACTIONr_angle_other_deg2.5371.57417302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.52751064
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91322.579411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.714151291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7191542
X-RAY DIFFRACTIONr_chiral_restr0.1280.21094
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.029346
X-RAY DIFFRACTIONr_gen_planes_other0.0260.021753
X-RAY DIFFRACTIONr_nbd_refined0.2260.21636
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2150.26915
X-RAY DIFFRACTIONr_nbtor_refined0.1760.23915
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23360
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2583
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1450.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3440.216
X-RAY DIFFRACTIONr_nbd_other0.3180.299
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1940.220
X-RAY DIFFRACTIONr_mcbond_it2.4641.9244071
X-RAY DIFFRACTIONr_mcbond_other2.4631.9254072
X-RAY DIFFRACTIONr_mcangle_it2.9972.9065108
X-RAY DIFFRACTIONr_mcangle_other2.9992.9065108
X-RAY DIFFRACTIONr_scbond_it3.7712.1154217
X-RAY DIFFRACTIONr_scbond_other3.7712.1164218
X-RAY DIFFRACTIONr_scangle_it4.8083.0896182
X-RAY DIFFRACTIONr_scangle_other4.8083.0886183
X-RAY DIFFRACTIONr_lrange_it5.43523.1659473
X-RAY DIFFRACTIONr_lrange_other5.26122.6399278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.402-1.4380.2597820.27115756X-RAY DIFFRACTION94.4867
1.438-1.4780.2567940.24816276X-RAY DIFFRACTION99.9941
1.478-1.520.2347750.22715786X-RAY DIFFRACTION100
1.52-1.5670.2268200.22115283X-RAY DIFFRACTION100
1.567-1.6190.2026690.20614988X-RAY DIFFRACTION100
1.619-1.6750.2037830.214332X-RAY DIFFRACTION100
1.675-1.7390.2047780.19213759X-RAY DIFFRACTION100
1.739-1.810.2028520.18613180X-RAY DIFFRACTION100
1.81-1.890.1928520.17812570X-RAY DIFFRACTION100
1.89-1.9820.1897450.1812115X-RAY DIFFRACTION99.9689
1.982-2.0890.1926880.1811569X-RAY DIFFRACTION99.9511
2.089-2.2160.1916770.17510830X-RAY DIFFRACTION99.9305
2.216-2.3690.1626580.15610203X-RAY DIFFRACTION99.9632
2.369-2.5590.1714780.159620X-RAY DIFFRACTION99.9406
2.559-2.8030.1524630.1468837X-RAY DIFFRACTION99.8175
2.803-3.1330.1694330.1567956X-RAY DIFFRACTION99.8334
3.133-3.6170.1763790.1627044X-RAY DIFFRACTION99.7581
3.617-4.4280.1423500.1345860X-RAY DIFFRACTION99.679
4.428-6.2540.1542700.1514569X-RAY DIFFRACTION99.7526
6.254-29.850.1771790.1912462X-RAY DIFFRACTION98.9509

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