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- PDB-6sxu: GH51 a-l-arabinofuranosidase soaked with cyclic sulfate inhibitor -

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Basic information

Entry
Database: PDB / ID: 6sxu
TitleGH51 a-l-arabinofuranosidase soaked with cyclic sulfate inhibitor
ComponentsIntracellular exo-alpha-(1->5)-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 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Chem-LX5 / DI(HYDROXYETHYL)ETHER / Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.398 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
BBB: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,77312
Polymers114,5702
Non-polymers1,20310
Water16,412911
1
AAA: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9106
Polymers57,2851
Non-polymers6255
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8646
Polymers57,2851
Non-polymers5795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)178.470, 178.470, 100.411
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 AAABBB

#1: Protein Intracellular exo-alpha-(1->5)-L-arabinofuranosidase / ABF / Intracellular arabinan exo-alpha-(1->5)-L-arabinosidase / Arabinosidase


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) / Strain (production host): Gold
References: UniProt: Q9XBQ3, non-reducing end alpha-L-arabinofuranosidase

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Non-polymers , 5 types, 921 molecules

#2: Chemical ChemComp-LX5 / [(1~{S},2~{S},3~{S},4~{S})-2-(hydroxymethyl)-3,4-bis(oxidanyl)cyclopentyl] hydrogen sulfate


Mass: 228.220 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 911 / 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 Matthews: 2.69 Å3/Da / Density % sol: 56.5 % / 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: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 21, 2018
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.398→29.75 Å / Num. obs: 235395 / % possible obs: 99.8 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Net I/σ(I): 18.7
Reflection shellResolution: 1.4→1.43 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 17031 / CC1/2: 0.776 / % possible all: 97.4

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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: 1.398→29.75 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.972 / Cross valid method: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.046
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.162 12421 5.277 %
Rwork0.1548 --
all0.155 --
obs-235394 99.762 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.403 Å2
Baniso -1Baniso -2Baniso -3
1-0.052 Å20.026 Å2-0 Å2
2--0.052 Å20 Å2
3----0.167 Å2
Refinement stepCycle: LAST / Resolution: 1.398→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7800 0 77 911 8788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0138266
X-RAY DIFFRACTIONr_bond_other_d0.0350.0177448
X-RAY DIFFRACTIONr_angle_refined_deg1.9961.64211292
X-RAY DIFFRACTIONr_angle_other_deg2.4371.57417258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10851055
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55722.67412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.372151319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3271541
X-RAY DIFFRACTIONr_chiral_restr0.4680.21091
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.029301
X-RAY DIFFRACTIONr_gen_planes_other0.0220.021742
X-RAY DIFFRACTIONr_nbd_refined0.2240.21597
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.26877
X-RAY DIFFRACTIONr_nbtor_refined0.1760.24009
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23506
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2577
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3470.212
X-RAY DIFFRACTIONr_nbd_other0.2780.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1170.235
X-RAY DIFFRACTIONr_mcbond_it2.0031.544056
X-RAY DIFFRACTIONr_mcbond_other1.9961.5394055
X-RAY DIFFRACTIONr_mcangle_it2.6812.3275081
X-RAY DIFFRACTIONr_mcangle_other2.6842.3285082
X-RAY DIFFRACTIONr_scbond_it3.431.7724210
X-RAY DIFFRACTIONr_scbond_other3.431.7724211
X-RAY DIFFRACTIONr_scangle_it4.7462.5636182
X-RAY DIFFRACTIONr_scangle_other4.7452.5646183
X-RAY DIFFRACTIONr_lrange_it5.4719.2019482
X-RAY DIFFRACTIONr_lrange_other5.29318.6089276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.398-1.4340.2327980.24216214X-RAY DIFFRACTION97.3115
1.434-1.4740.2467930.22216210X-RAY DIFFRACTION100
1.474-1.5160.2037820.20515803X-RAY DIFFRACTION99.994
1.516-1.5630.1998010.1915237X-RAY DIFFRACTION99.9875
1.563-1.6140.1816790.17514908X-RAY DIFFRACTION99.9872
1.614-1.6710.1747770.16714262X-RAY DIFFRACTION100
1.671-1.7340.1647870.15913747X-RAY DIFFRACTION100
1.734-1.8050.1668440.1613154X-RAY DIFFRACTION100
1.805-1.8850.1698590.1512516X-RAY DIFFRACTION100
1.885-1.9770.1687320.15412082X-RAY DIFFRACTION99.9766
1.977-2.0840.1666820.15511553X-RAY DIFFRACTION100
2.084-2.210.1726860.15210798X-RAY DIFFRACTION100
2.21-2.3630.1376500.13910195X-RAY DIFFRACTION99.9908
2.363-2.5520.1434820.139623X-RAY DIFFRACTION100
2.552-2.7950.1384600.1338788X-RAY DIFFRACTION99.9892
2.795-3.1250.1594290.1487963X-RAY DIFFRACTION100
3.125-3.6070.1563780.1527032X-RAY DIFFRACTION99.973
3.607-4.4160.1323520.1265862X-RAY DIFFRACTION100
4.416-6.2380.1672700.1524577X-RAY DIFFRACTION100
6.238-29.750.1711800.1982449X-RAY DIFFRACTION99.0207

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