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- PDB-8qce: Dispersin from Lactiplantibacillus paraplantarum DispLp -

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Basic information

Entry
Database: PDB / ID: 8qce
TitleDispersin from Lactiplantibacillus paraplantarum DispLp
ComponentsN-acetyl-beta-hexosaminidase
KeywordsHYDROLASE / biofilm degradation / GH20 / poly-N-acetylglucosamine / enzyme catalysis
Function / homology6-ACETAMIDO-6-DEOXY-CASTANOSPERMINE / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesLactiplantibacillus paraplantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 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 25, 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: N-acetyl-beta-hexosaminidase
B: N-acetyl-beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5678
Polymers74,8142
Non-polymers7536
Water13,908772
1
A: N-acetyl-beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7614
Polymers37,4071
Non-polymers3543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-acetyl-beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8064
Polymers37,4071
Non-polymers3983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.902, 82.792, 80.642
Angle α, β, γ (deg.)90.000, 98.115, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: SER / End label comp-ID: SER / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: -1 - 330 / Label seq-ID: 4 - 335

Dom-ID
1
2

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

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Components

#1: Protein N-acetyl-beta-hexosaminidase


Mass: 37407.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactiplantibacillus paraplantarum (bacteria)
Gene: DQM08_04690 / Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A370AE65
#2: Chemical ChemComp-GC2 / 6-ACETAMIDO-6-DEOXY-CASTANOSPERMINE / N-[(1S,6S,7R,8R,8AR)-1,7,8-TRIHYDROXYOCTAHYDROINDOLIZIN-6-YL]ACETAMIDE


Mass: 230.261 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 772 / 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: 2.07 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M calcium chloride, 0.1 M sodium acetate pH 5.0, 20% PEG 6000 (PACT A10), MMS from Hampton D10

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.05→38.06 Å / Num. obs: 256432 / % possible obs: 90.5 % / Redundancy: 3.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.068 / Rrim(I) all: 0.105 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
5.75-38.063.90.06370230.9910.0540.084
1.05-1.072.21.052125830.4220.931.411

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.05→38.057 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.672 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.03
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1696 12700 4.954 %
Rwork0.1474 243670 -
all0.148 --
obs-256370 90.547 %
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: 13.86 Å2
Baniso -1Baniso -2Baniso -3
1-1.303 Å20 Å20.098 Å2
2--0.824 Å2-0 Å2
3----2.071 Å2
Refinement stepCycle: LAST / Resolution: 1.05→38.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5246 0 51 772 6069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0125746
X-RAY DIFFRACTIONr_bond_other_d0.0030.0165185
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.6567881
X-RAY DIFFRACTIONr_angle_other_deg0.6881.57911919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6375724
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.105522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35710882
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.10410294
X-RAY DIFFRACTIONr_chiral_restr0.0950.2908
X-RAY DIFFRACTIONr_chiral_restr_other0.0020.21
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026974
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021346
X-RAY DIFFRACTIONr_nbd_refined0.2350.21118
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.24742
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22717
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.22922
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2581
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1010.219
X-RAY DIFFRACTIONr_nbd_other0.1740.281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1630.246
X-RAY DIFFRACTIONr_mcbond_it3.7471.3322848
X-RAY DIFFRACTIONr_mcbond_other3.7361.3322848
X-RAY DIFFRACTIONr_mcangle_it5.2392.43588
X-RAY DIFFRACTIONr_mcangle_other5.2422.43589
X-RAY DIFFRACTIONr_scbond_it18.0571.5492898
X-RAY DIFFRACTIONr_scbond_other18.0541.552899
X-RAY DIFFRACTIONr_scangle_it16.8712.7514293
X-RAY DIFFRACTIONr_scangle_other16.8712.7524294
X-RAY DIFFRACTIONr_lrange_it22.19518.3336612
X-RAY DIFFRACTIONr_lrange_other22.19418.3336613
X-RAY DIFFRACTIONr_rigid_bond_restr5.912310931
X-RAY DIFFRACTIONr_ncsr_local_group_10.0910.0511568
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.091150.05008
12AX-RAY DIFFRACTIONLocal ncs0.091150.05008
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
1.05-1.0770.3464430.3384320.331209080.9490.95642.44790.329
1.077-1.1070.3225460.293111140.295203470.950.96557.30570.288
1.107-1.1390.287480.264141850.265198060.9620.97175.39630.255
1.139-1.1740.2619890.245175950.246192260.970.97496.66080.233
1.174-1.2120.2329050.215175960.216185790.9710.98199.58020.203
1.212-1.2550.2159370.192171000.193180880.9770.98599.7180.179
1.255-1.3020.2038760.177165220.178174470.9790.98799.71910.164
1.302-1.3550.1867750.163158710.164166990.9840.98999.68260.152
1.355-1.4150.1927850.151152590.153160770.980.9999.79470.141
1.415-1.4840.1697470.137145830.138153540.9860.99299.84370.129
1.484-1.5650.1577300.124139080.125146740.9880.99399.75470.119
1.565-1.6590.1666790.125130690.127137680.9850.99399.85470.123
1.659-1.7740.1576050.123123960.124130180.9870.99399.86940.124
1.774-1.9150.1555920.124115180.126121300.9850.99299.83510.13
1.915-2.0980.1545810.124105500.126111550.9870.99299.78490.134
2.098-2.3440.1465330.1295680.121101270.9880.99299.74330.135
2.344-2.7050.1443790.11985140.1289180.9880.99299.71970.138
2.705-3.3090.1444130.12871620.12976020.9880.9999.64480.152
3.309-4.6620.1372840.13155720.13258780.9890.9999.62570.163
4.662-38.0570.1671520.1831570.1833280.9840.98599.42910.224

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