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- PDB-8qak: Dispersin from Terribacillus saccharophilus DispTs3 -

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Basic information

Entry
Database: PDB / ID: 8qak
TitleDispersin from Terribacillus saccharophilus DispTs3
ComponentsGlycoside hydrolase family 20 catalytic domain-containing protein
KeywordsHYDROLASE / biofilm degradation / GH20 / poly-N-acetylglucosamine / enzyme catalysis
Function / homology: / Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / beta-N-acetylglucosaminidase activity / Glycoside hydrolase superfamily / carbohydrate metabolic process / ACETATE ION / Glycoside hydrolase family 20 catalytic domain-containing protein
Function and homology information
Biological speciesTerribacillus saccharophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMales, A. / Moroz, O.V. / Blagova, E. / Munch, A. / Hansen, G.H. / Johansen, A.H. / Ostergaard, L.H. / Segura, D.R. / Eddenden, A. / Due, A.V. ...Males, A. / Moroz, O.V. / Blagova, E. / Munch, A. / Hansen, G.H. / Johansen, A.H. / Ostergaard, L.H. / Segura, D.R. / Eddenden, A. / Due, A.V. / Gudmand, M. / Salomon, J. / Sorensen, S.R. / Cairo, J.L.F. / Pache, R.A. / Vejborg, R.M. / Davies, G.J. / Wilson, K.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2025
Title: Expansion of the diversity of dispersin scaffolds.
Authors: Males, A. / Moroz, O.V. / Blagova, E. / Munch, A. / Hansen, G.H. / Johansen, A.H. / Ostergaard, L.H. / Segura, D.R. / Eddenden, A. / Due, A.V. / Gudmand, M. / Salomon, J. / Sorensen, S.R. / ...Authors: Males, A. / Moroz, O.V. / Blagova, E. / Munch, A. / Hansen, G.H. / Johansen, A.H. / Ostergaard, L.H. / Segura, D.R. / Eddenden, A. / Due, A.V. / Gudmand, M. / Salomon, J. / Sorensen, S.R. / Franco Cairo, J.P.L. / Nitz, M. / Pache, R.A. / Vejborg, R.M. / Bhosale, S. / Vocadlo, D.J. / Davies, G.J. / Wilson, K.S.
History
DepositionAug 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 20 catalytic domain-containing protein
B: Glycoside hydrolase family 20 catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2304
Polymers74,1122
Non-polymers1182
Water5,999333
1
A: Glycoside hydrolase family 20 catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1152
Polymers37,0561
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 20 catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1152
Polymers37,0561
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.948, 109.352, 131.084
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: GLN / Beg label comp-ID: GLN / End auth comp-ID: GLY / End label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 3 - 323 / Label seq-ID: 3 - 323

Dom-ID
1
2

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

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Components

#1: Protein Glycoside hydrolase family 20 catalytic domain-containing protein / Family 20 Beta-Hexosaminidase


Mass: 37055.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Family 20 Beta-Hexosaminidase
Source: (gene. exp.) Terribacillus saccharophilus (bacteria)
Gene: GZ22_15930 / Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A075LPR4
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morpheus B3, 0.09 M Halogens, 30% glycerol/PEG4000 mix, from Microseed matrix screening

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.95→83.97 Å / Num. obs: 54127 / % possible obs: 99.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 23.7 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.108 / Rrim(I) all: 0.183 / Net I/σ(I): 7.3
Reflection shellResolution: 1.95→2 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.401 / Mean I/σ(I) obs: 1 / Num. unique obs: 3734 / CC1/2: 0.341 / Rpim(I) all: 1.047 / Rrim(I) all: 1.758

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→83.97 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.34 / SU ML: 0.154 / Cross valid method: FREE R-VALUE / ESU R: 0.163 / ESU R Free: 0.146
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.224 2624 4.853 %
Rwork0.1888 51445 -
all0.191 --
obs-54069 99.628 %
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: 31.211 Å2
Baniso -1Baniso -2Baniso -3
1--1.896 Å2-0 Å20 Å2
2--3.178 Å2-0 Å2
3----1.283 Å2
Refinement stepCycle: LAST / Resolution: 1.95→83.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5212 0 8 333 5553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0125324
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164829
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.6567223
X-RAY DIFFRACTIONr_angle_other_deg0.7261.57811135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.8595643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.519512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49710890
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.99410276
X-RAY DIFFRACTIONr_chiral_restr0.0850.2772
X-RAY DIFFRACTIONr_chiral_restr_other0.3060.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026295
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021253
X-RAY DIFFRACTIONr_nbd_refined0.2350.21067
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.24567
X-RAY DIFFRACTIONr_nbtor_refined0.1940.22664
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.22796
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2337
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1060.210
X-RAY DIFFRACTIONr_nbd_other0.1960.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2790.29
X-RAY DIFFRACTIONr_mcbond_it3.3213.0732580
X-RAY DIFFRACTIONr_mcbond_other3.3183.0732578
X-RAY DIFFRACTIONr_mcangle_it4.3555.5043219
X-RAY DIFFRACTIONr_mcangle_other4.3585.5053220
X-RAY DIFFRACTIONr_scbond_it5.0063.5092744
X-RAY DIFFRACTIONr_scbond_other5.0053.5092745
X-RAY DIFFRACTIONr_scangle_it7.2786.2294004
X-RAY DIFFRACTIONr_scangle_other7.2776.2294005
X-RAY DIFFRACTIONr_lrange_it9.03131.5276208
X-RAY DIFFRACTIONr_lrange_other9.03131.5266209
X-RAY DIFFRACTIONr_ncsr_local_group_10.0940.0511064
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.093560.05008
12AX-RAY DIFFRACTIONLocal ncs0.093560.05008
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
1.95-2.0010.3661850.35237460.35239420.8670.87399.7210.337
2.001-2.0550.3281600.32936880.32938560.9050.88899.79250.304
2.055-2.1150.3371840.29935660.30137580.890.91199.78710.268
2.115-2.180.2921860.28434400.28536290.9170.92399.91730.253
2.18-2.2510.2831700.25433630.25535360.9290.93999.91520.218
2.251-2.330.2531670.2432770.24134490.9430.94899.8550.204
2.33-2.4180.2751680.22431440.22633210.9270.95799.7290.185
2.418-2.5170.231670.21330270.21431970.9540.96499.90620.176
2.517-2.6290.2631420.2229010.22130520.9480.96799.70510.183
2.629-2.7570.2711530.20827730.21129330.9520.97299.76130.173
2.757-2.9060.2211410.17726380.1827810.9690.97999.92810.147
2.906-3.0820.2211230.17225270.17426710.9680.9899.21380.146
3.082-3.2940.2311190.17423860.17625100.9610.98199.80080.154
3.294-3.5580.2181120.17322250.17523430.9690.98399.74390.158
3.558-3.8970.1941080.15320470.15521710.980.98999.2630.144
3.897-4.3560.153980.12118350.12219610.9880.99298.57220.116
4.356-5.0270.136830.10716740.10817640.9920.99499.60320.102
5.027-6.1520.178680.13614090.13814870.9830.99199.32750.127
6.152-8.6760.15550.13311260.13411990.9850.9998.49870.129
8.676-83.970.191350.1486530.157110.9830.98596.76510.149

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