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- PDB-9hmb: Crystal structure of GH139 glycoside hydrolase from Verrucomicrob... -

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Basic information

Entry
Database: PDB / ID: 9hmb
TitleCrystal structure of GH139 glycoside hydrolase from Verrucomicrobium sp. in the hexagonal space group P6522
ComponentsDUF5703 domain-containing protein
KeywordsHYDROLASE / alpha-L-fucosidase glycosyl hydrolase GH139
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 speciesVerrucomicrobium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMoraleda-Montoya, A. / Garcia-Alija, M. / Trastoy, B. / Guerin, M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO) Spain
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Understanding the substrate recognition and catalytic mechanism of 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
DepositionDec 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF5703 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8313
Polymers88,6471
Non-polymers1842
Water12,773709
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-1 kcal/mol
Surface area28840 Å2
Unit cell
Length a, b, c (Å)209.450, 209.450, 143.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein DUF5703 domain-containing protein


Mass: 88646.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Verrucomicrobium sp. (bacteria) / Gene: SAMN05444156_0716 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1H2E9C4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 709 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 5.15 Å3/Da / Density % sol: 76.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium citrate tribasic dihydrate, 0.1 M Bis-Tris propane pH 8.5 and 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.05→76.74 Å / Num. obs: 222324 / % possible obs: 99.96 % / Redundancy: 39.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 71.7
Reflection shellResolution: 2.05→2.123 Å / Num. unique obs: 5422 / Rrim(I) all: 0.789

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→76.74 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1719 11125 5 %
Rwork0.1328 --
obs0.1347 222324 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→76.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6234 0 12 709 6955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096427
X-RAY DIFFRACTIONf_angle_d0.9538770
X-RAY DIFFRACTIONf_dihedral_angle_d6.159888
X-RAY DIFFRACTIONf_chiral_restr0.051932
X-RAY DIFFRACTIONf_plane_restr0.011167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.070.23353650.17846960X-RAY DIFFRACTION99
2.07-2.10.20273770.15867085X-RAY DIFFRACTION100
2.1-2.120.22323660.16657053X-RAY DIFFRACTION100
2.12-2.150.22843700.15917029X-RAY DIFFRACTION100
2.15-2.180.1923690.15417015X-RAY DIFFRACTION100
2.18-2.210.19043730.14397047X-RAY DIFFRACTION100
2.21-2.240.15483720.13167053X-RAY DIFFRACTION100
2.24-2.270.17673750.13037063X-RAY DIFFRACTION100
2.27-2.310.18313660.12417001X-RAY DIFFRACTION100
2.31-2.340.16933750.12567020X-RAY DIFFRACTION100
2.34-2.380.16443640.12477046X-RAY DIFFRACTION100
2.38-2.430.16933720.12527052X-RAY DIFFRACTION100
2.43-2.470.17473710.11987049X-RAY DIFFRACTION100
2.47-2.520.16633750.12347047X-RAY DIFFRACTION100
2.52-2.580.17783760.12047054X-RAY DIFFRACTION100
2.58-2.640.17093710.12327005X-RAY DIFFRACTION100
2.64-2.710.19643730.13157034X-RAY DIFFRACTION100
2.71-2.780.18583720.13957056X-RAY DIFFRACTION100
2.78-2.860.19133680.14327058X-RAY DIFFRACTION100
2.86-2.950.18353710.13487047X-RAY DIFFRACTION100
2.95-3.060.18323710.13477026X-RAY DIFFRACTION100
3.06-3.180.18043630.14277069X-RAY DIFFRACTION100
3.18-3.330.19623720.15467022X-RAY DIFFRACTION100
3.33-3.50.17363780.14597028X-RAY DIFFRACTION100
3.5-3.720.18563720.12947060X-RAY DIFFRACTION100
3.72-4.010.1423680.11717044X-RAY DIFFRACTION100
4.01-4.410.12463700.10397029X-RAY DIFFRACTION100
4.41-5.050.12853700.1037055X-RAY DIFFRACTION100
5.05-6.360.17373680.13017066X-RAY DIFFRACTION100
6.36-76.740.18223720.16617026X-RAY DIFFRACTION100

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