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- PDB-9hyq: BT984 a GH139 rhamnogalacturonan II exo-a-1,2-(2-Omethyl)-fucosidase -

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Basic information

Entry
Database: PDB / ID: 9hyq
TitleBT984 a GH139 rhamnogalacturonan II exo-a-1,2-(2-Omethyl)-fucosidase
ComponentsDUF5703 domain-containing protein
KeywordsHYDROLASE / Glycoside hydrolases / GH139 / Microbiota / fucosidase / inverting
Function / homologyDomain of unknown function DUF5703 / Domain of unknown function (DUF5703) / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyl hydrolase, all-beta / carbohydrate metabolic process / DUF5703 domain-containing protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCartmell, A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Royal Society212050 United Kingdom
Wellcome Trust1065163470 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Understanding the substrate recognition and catalytic mechanism of 2-O-methyl fucosidases from glycoside hydrolase family 139.
Authors: McIver, Z. / Moraleda-Montoya, A. / Chen, Z. / Epa, R. / Starns, D. / Davy, M. / Garcia-Alija, M. / Basle, A. / Schubert, M. / Ndeh, D. / Trastoy, B. / Williams, S.J. / Guerin, M.E. / Cartmell, A.
History
DepositionJan 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF5703 domain-containing protein
B: DUF5703 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)184,8602
Polymers184,8602
Non-polymers00
Water21612
1
A: DUF5703 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)92,4301
Polymers92,4301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DUF5703 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)92,4301
Polymers92,4301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.201, 138.322, 195.53
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 21 - 801 / Label seq-ID: 20 - 800

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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

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Components

#1: Protein DUF5703 domain-containing protein


Mass: 92430.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_0984 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A933
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.6 Å3/Da / Density % sol: 52.69 % / Description: Cubes
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG 3000 0.1 M Tris pH8.5 10 mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→47.478 Å / Num. obs: 75053 / % possible obs: 98.9 % / Redundancy: 3.3 % / CC1/2: 0.997 / Net I/σ(I): 10.4
Reflection shellResolution: 2.7→2.76 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4450 / CC1/2: 0.502

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→47.478 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 21.976 / SU ML: 0.364 / Cross valid method: FREE R-VALUE / ESU R: 0.442 / ESU R Free: 0.292
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2557 3736 4.98 %
Rwork0.2182 71280 -
all0.22 --
obs-75016 98.633 %
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: 76.237 Å2
Baniso -1Baniso -2Baniso -3
1--5.108 Å2-0 Å20 Å2
2---6.85 Å2-0 Å2
3---11.958 Å2
Refinement stepCycle: LAST / Resolution: 2.7→47.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12169 0 0 12 12181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01212522
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611476
X-RAY DIFFRACTIONr_angle_refined_deg1.41.81616979
X-RAY DIFFRACTIONr_angle_other_deg0.5041.77126442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96851484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.673572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.997102097
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.2310626
X-RAY DIFFRACTIONr_chiral_restr0.070.21746
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214980
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023096
X-RAY DIFFRACTIONr_nbd_refined0.2210.22449
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.210668
X-RAY DIFFRACTIONr_nbtor_refined0.1880.26016
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.26294
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0490.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1810.218
X-RAY DIFFRACTIONr_nbd_other0.2490.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3440.24
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2510.21
X-RAY DIFFRACTIONr_mcbond_it5.6647.4045960
X-RAY DIFFRACTIONr_mcbond_other5.6627.4045960
X-RAY DIFFRACTIONr_mcangle_it8.713.2877436
X-RAY DIFFRACTIONr_mcangle_other8.713.2877437
X-RAY DIFFRACTIONr_scbond_it5.4547.8276562
X-RAY DIFFRACTIONr_scbond_other5.4547.8286563
X-RAY DIFFRACTIONr_scangle_it8.6814.1979543
X-RAY DIFFRACTIONr_scangle_other8.67914.1979544
X-RAY DIFFRACTIONr_lrange_it11.47870.84813869
X-RAY DIFFRACTIONr_lrange_other11.47870.8513870
X-RAY DIFFRACTIONr_ncsr_local_group_10.0890.0525494
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.089380.0501
12BX-RAY DIFFRACTIONLocal ncs0.089380.0501
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
2.7-2.770.4543020.41552030.41755390.6870.799.38620.408
2.77-2.8460.4322680.39851080.454120.770.76599.33480.381
2.846-2.9280.3492590.38149290.3852340.8470.84299.12110.361
2.928-3.0170.3722550.35648520.35751220.8370.85599.70710.331
3.017-3.1160.3582290.34747170.34749630.880.86899.65750.316
3.116-3.2250.3412590.31744970.31847830.890.89699.43550.287
3.225-3.3460.3462090.29544130.29746520.8910.91699.35510.266
3.346-3.4820.2722130.24742050.24844650.9430.94598.94740.22
3.482-3.6360.2622290.22340060.22643020.9380.9698.44260.199
3.636-3.8120.2211850.19238670.19340970.9640.97298.90160.173
3.812-4.0170.251850.18536790.18839330.9410.97598.24560.17
4.017-4.2590.221980.16734570.1737030.9630.97998.70380.153
4.259-4.550.1711680.14832630.14935070.9820.98597.83290.138
4.55-4.9110.2171420.15530770.15832920.9720.98497.78250.148
4.911-5.3740.1861440.14128190.14430160.9790.98798.24270.134
5.374-5.9990.1851420.14925650.1527580.9810.98798.15080.139
5.999-6.9080.257990.18122660.18424480.9670.98196.60950.17
6.908-8.4170.2391160.1719100.17421050.9620.98296.2470.172
8.417-11.720.15820.14915270.14916730.9850.98896.17450.163
11.72-47.4780.284520.2679200.26810310.9450.9594.27740.303

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