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- PDB-8qk1: Crystal structure of Trichuris suis beta-N-acetyl-D-hexosaminidas... -

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Basic information

Entry
Database: PDB / ID: 8qk1
TitleCrystal structure of Trichuris suis beta-N-acetyl-D-hexosaminidase - HEX-2 in apo form
Componentsbeta-N-acetylhexosaminidase
KeywordsHYDROLASE / hexosaminidase / enzyme / Glycoside Hydrolase Family 20
Function / homology
Function and homology information


beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / carbohydrate metabolic process / membrane
Similarity search - Function
Hexosaminidase D-like / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesTrichuris suis (pig whipworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsDutkiewicz, Z. / Varrot, A.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundW1224 Austria
CitationJournal: To be published
Title: Nematode hexosaminidases, a new biochemical tool for glycan analysis
Authors: Dutkiewicz, Z. / Varrot, A. / Wilson, I.
History
DepositionSep 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3352
Polymers63,2691
Non-polymers651
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-35 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.118, 59.044, 105.977
Angle α, β, γ (deg.)90.000, 114.486, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein beta-N-acetylhexosaminidase


Mass: 63269.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichuris suis (pig whipworm) / Gene: M514_07548 / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115 / References: UniProt: A0A085NCI8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 1500 0.15M potasium thiocynate 0.1M Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.55→43.74 Å / Num. obs: 17835 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 59.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.043 / Rrim(I) all: 0.08 / Net I/σ(I): 14.1
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2157 / CC1/2: 0.843 / Rpim(I) all: 0.5 / Rrim(I) all: 0.931 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimless0.7.9data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→43.74 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.907 / SU B: 12.767 / SU ML: 0.269 / Cross valid method: FREE R-VALUE / ESU R: 0.785 / ESU R Free: 0.324
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2594 836 4.841 %
Rwork0.1894 16432 -
all0.193 --
obs-17268 96.734 %
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: 42.658 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å2-0.307 Å2
2--0.12 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.55→43.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3688 0 1 44 3733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123789
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163519
X-RAY DIFFRACTIONr_angle_refined_deg1.9961.6515147
X-RAY DIFFRACTIONr_angle_other_deg0.641.5818073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.155454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.398521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.45110623
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.77110185
X-RAY DIFFRACTIONr_chiral_restr0.0860.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024467
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02913
X-RAY DIFFRACTIONr_nbd_refined0.2490.2864
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2380.23555
X-RAY DIFFRACTIONr_nbtor_refined0.2050.21875
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.22110
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2100
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1260.223
X-RAY DIFFRACTIONr_nbd_other0.1870.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3220.27
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0930.24
X-RAY DIFFRACTIONr_mcbond_it5.8554.1941822
X-RAY DIFFRACTIONr_mcbond_other5.8534.1941822
X-RAY DIFFRACTIONr_mcangle_it8.1227.5212274
X-RAY DIFFRACTIONr_mcangle_other8.127.5222275
X-RAY DIFFRACTIONr_scbond_it6.6644.5651967
X-RAY DIFFRACTIONr_scbond_other6.6634.5661968
X-RAY DIFFRACTIONr_scangle_it9.3318.1762873
X-RAY DIFFRACTIONr_scangle_other9.3298.1772874
X-RAY DIFFRACTIONr_lrange_it11.45242.154319
X-RAY DIFFRACTIONr_lrange_other11.45442.1594318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.6160.338560.289937X-RAY DIFFRACTION77.3967
2.616-2.6870.312510.291052X-RAY DIFFRACTION84.3272
2.687-2.7650.295520.251085X-RAY DIFFRACTION94.0447
2.765-2.850.281730.2371134X-RAY DIFFRACTION99.5875
2.85-2.9430.362670.2341106X-RAY DIFFRACTION99.9148
2.943-3.0460.38580.2311071X-RAY DIFFRACTION100
3.046-3.160.348410.2021044X-RAY DIFFRACTION100
3.16-3.2880.269570.207995X-RAY DIFFRACTION100
3.288-3.4340.281540.214946X-RAY DIFFRACTION100
3.434-3.60.334450.211929X-RAY DIFFRACTION99.8974
3.6-3.7940.302330.212884X-RAY DIFFRACTION99.8911
3.794-4.0220.287380.172854X-RAY DIFFRACTION100
4.022-4.2970.182380.145763X-RAY DIFFRACTION100
4.297-4.6370.188200.13747X-RAY DIFFRACTION100
4.637-5.0740.172350.14679X-RAY DIFFRACTION100
5.074-5.6640.239220.158623X-RAY DIFFRACTION99.8452
5.664-6.5220.276280.165530X-RAY DIFFRACTION99.6429

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