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- PDB-8qf8: GH146 beta-L-arabinofuranosidase from Bacteroides thetaioatomicro... -

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Basic information

Entry
Database: PDB / ID: 8qf8
TitleGH146 beta-L-arabinofuranosidase from Bacteroides thetaioatomicron in complex with beta-l-arabinofurano cyclophellitol aziridine
ComponentsGlycosyl hydrolase
KeywordsHYDROLASE / btGH146 / inhibitors / fluorescent probes
Function / homology
Function and homology information


carbohydrate metabolic process / hydrolase activity / metal ion binding
Similarity search - Function
Domain of unknown function DUF4986 / Domain of unknown function DUF6805 / Domain of unknown function / Family of unknown function (DUF6805) / Beta-L-arabinofuranosidase, GH127 / : / Beta-L-arabinofuranosidase, GH127 catalytic domain / Beta-L-arabinofuranosidase, GH127 middle domain / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
Chem-UHU / Chem-UI5 / Glycosyl hydrolase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBorlandelli, V. / Offen, W. / Moroz, O.V. / Nin-Hill, A. / McGregor, N. / Binkhorst, L. / Armstrong, Z. / Ishiwata, A. / Artola, M. / Rovira, C. ...Borlandelli, V. / Offen, W. / Moroz, O.V. / Nin-Hill, A. / McGregor, N. / Binkhorst, L. / Armstrong, Z. / Ishiwata, A. / Artola, M. / Rovira, C. / Davies, G.J. / Overkleeft, H.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)951231European Union
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: beta-l- Arabino furano-cyclitol Aziridines Are Covalent Broad-Spectrum Inhibitors and Activity-Based Probes for Retaining beta-l-Arabinofuranosidases.
Authors: Borlandelli, V. / Offen, W. / Moroz, O. / Nin-Hill, A. / McGregor, N. / Binkhorst, L. / Ishiwata, A. / Armstrong, Z. / Artola, M. / Rovira, C. / Davies, G.J. / Overkleeft, H.S.
History
DepositionSep 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 6, 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: Glycosyl hydrolase
B: Glycosyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,3486
Polymers182,9252
Non-polymers4234
Water5,621312
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint3 kcal/mol
Surface area57950 Å2
Unit cell
Length a, b, c (Å)93.840, 98.549, 196.584
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LYS / End label comp-ID: LYS / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 22 - 802 / Label seq-ID: 22 - 802

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Glycosyl hydrolase


Mass: 91462.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: GAN91_19850 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6I0SRL5
#2: Chemical ChemComp-UI5 / (1~{S},2~{S},3~{S},4~{R})-4-azanyl-3-(hydroxymethyl)cyclopentane-1,2-diol


Mass: 147.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-UHU / (1~{S},2~{S},3~{S},4~{S},5~{S})-4-(hydroxymethyl)-6-azabicyclo[3.1.0]hexane-2,3-diol


Mass: 145.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 15-17% PEG 3350, MES pH 6.25-6.5, 0.2M ammonium formate, seeding from similar conditions

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.4→55.9 Å / Num. obs: 72064 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.041 / Rrim(I) all: 0.109 / Net I/σ(I): 16.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
11.76-55.912.10.0297730.9910.0130.032
2.4-2.4512.71.13853080.830.4811.237

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
REFMAC5.8.0419refinement
DIALSdata collection
Aimlessdata scaling
MOLREPphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→55.899 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.945 / SU B: 17.765 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.397 / ESU R Free: 0.233
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2208 3622 5.032 %
Rwork0.1896 68360 -
all0.191 --
obs-71982 99.963 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 61.794 Å2
Baniso -1Baniso -2Baniso -3
1-3.914 Å20 Å20 Å2
2---1.045 Å20 Å2
3----2.868 Å2
Refinement stepCycle: LAST / Resolution: 2.4→55.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12421 0 22 312 12755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01212756
X-RAY DIFFRACTIONr_bond_other_d0.0020.01611763
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.67117292
X-RAY DIFFRACTIONr_angle_other_deg0.4921.58827084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08551542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.964580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.437102149
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.08610627
X-RAY DIFFRACTIONr_chiral_restr0.0620.21856
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215126
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023030
X-RAY DIFFRACTIONr_nbd_refined0.1830.22128
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1530.210314
X-RAY DIFFRACTIONr_nbtor_refined0.1630.26027
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0670.26486
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2476
X-RAY DIFFRACTIONr_metal_ion_refined0.1340.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1480.216
X-RAY DIFFRACTIONr_nbd_other0.1440.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.180.212
X-RAY DIFFRACTIONr_mcbond_it2.0163.7746183
X-RAY DIFFRACTIONr_mcbond_other2.0163.7746183
X-RAY DIFFRACTIONr_mcangle_it3.1346.7997720
X-RAY DIFFRACTIONr_mcangle_other3.1346.7997721
X-RAY DIFFRACTIONr_scbond_it2.313.9786573
X-RAY DIFFRACTIONr_scbond_other2.3093.9786574
X-RAY DIFFRACTIONr_scangle_it3.7427.2159569
X-RAY DIFFRACTIONr_scangle_other3.7417.2159570
X-RAY DIFFRACTIONr_lrange_it6.05745.55954157
X-RAY DIFFRACTIONr_lrange_other6.05245.54854044
X-RAY DIFFRACTIONr_ncsr_local_group_10.0640.0526238
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.064140.0501
12AX-RAY DIFFRACTIONLocal ncs0.064140.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.4-2.4620.3482820.27949540.28252380.9250.94599.96180.251
2.462-2.530.2722500.2748760.2751280.9520.95199.9610.239
2.53-2.6030.2642480.24847320.24949800.9550.9611000.216
2.603-2.6830.2772340.2446070.24248410.9530.9661000.209
2.683-2.770.2952740.23144160.23546900.9510.9691000.197
2.77-2.8670.2642610.21642870.21845480.9590.9721000.183
2.867-2.9750.2642180.21241700.21543880.9590.9731000.185
2.975-3.0960.2312170.21640220.21742390.9630.971000.19
3.096-3.2340.2741680.2239190.22240870.9510.9691000.199
3.234-3.3910.261960.2136810.21238770.960.9731000.191
3.391-3.5740.2031860.2135430.20937290.9770.9771000.195
3.574-3.790.2381720.19133480.19335220.9670.98199.94320.176
3.79-4.050.2041540.16231550.16433090.9770.9851000.149
4.05-4.3720.1841570.14729360.14930930.9810.9871000.135
4.372-4.7870.1611530.13227200.13328730.9840.991000.123
4.787-5.3470.1881500.14724540.1526060.980.98899.92330.138
5.347-6.1650.2181140.1822170.18223320.9730.98499.95710.167
6.165-7.5270.208790.17718920.17919820.9760.98199.4450.168
7.527-10.550.146730.13815070.13815800.9860.9881000.133
10.55-55.8990.196360.2469230.2449590.9720.9241000.236
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0543-0.22290.10651.79180.98752.23590.00550.1408-0.0765-0.2377-0.28480.2315-0.0256-0.29690.27930.05780.0124-0.0160.0802-0.05960.0486-8.2895-36.898821.6665
21.94590.25010.63861.18860.49831.7833-0.12710.21890.2413-0.218-0.0025-0.041-0.1341-0.01290.12960.0855-0.0274-0.01020.1011-0.05570.1553-37.3928-71.269629.0003
Refinement TLS groupSelection: ALL

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