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- PDB-8qb6: Dispersin from Terribacillus saccharophilus DispTs2 -

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Basic information

Entry
Database: PDB / ID: 8qb6
TitleDispersin from Terribacillus saccharophilus DispTs2
ComponentsDispersin
KeywordsHYDROLASE / biofilm degradation / GH20 / poly-N-acetylglucosamine / enzyme catalysis
Function / homology6-ACETAMIDO-6-DEOXY-CASTANOSPERMINE
Function and homology information
Biological speciesTerribacillus saccharophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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 24, 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

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Assembly

Deposited unit
A: Dispersin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0294
Polymers37,5621
Non-polymers4673
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-16 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.688, 89.688, 97.685
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-677-

HOH

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Components

#1: Protein Dispersin


Mass: 37562.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Terribacillus saccharophilus (bacteria)
Production host: Bacillus subtilis (bacteria)
#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.: 1 / Source method: obtained synthetically / Formula: C10H18N2O4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 3.02 Å3/Da / Density % sol: 59.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: MPD screen E7: 0.1 M Citric acid pH 4.0, 20% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.51→30.4 Å / Num. obs: 71635 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.027 / Rrim(I) all: 0.062 / Net I/σ(I): 17.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.27-30.48.40.0334920.9980.0170.037
1.51-1.54101.76435220.510.861.966

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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: 1.51→30.398 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.974 / SU B: 4.211 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1784 3623 5.061 %
Rwork0.1534 67969 -
all0.155 --
obs-71592 99.98 %
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: 26.325 Å2
Baniso -1Baniso -2Baniso -3
1--1.493 Å2-0.747 Å20 Å2
2---1.493 Å2-0 Å2
3---4.844 Å2
Refinement stepCycle: LAST / Resolution: 1.51→30.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2621 0 32 198 2851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122772
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162457
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.6583786
X-RAY DIFFRACTIONr_angle_other_deg0.5621.585669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.795336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.81755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93710445
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.93610146
X-RAY DIFFRACTIONr_chiral_restr0.0810.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023281
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02643
X-RAY DIFFRACTIONr_nbd_refined0.2280.2528
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.22334
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21393
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21398
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2189
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1220.215
X-RAY DIFFRACTIONr_nbd_other0.210.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1230.221
X-RAY DIFFRACTIONr_mcbond_it7.9562.7141326
X-RAY DIFFRACTIONr_mcbond_other7.9472.7141326
X-RAY DIFFRACTIONr_mcangle_it10.4664.8921668
X-RAY DIFFRACTIONr_mcangle_other10.4644.8921669
X-RAY DIFFRACTIONr_scbond_it9.4712.9161446
X-RAY DIFFRACTIONr_scbond_other9.4682.9171447
X-RAY DIFFRACTIONr_scangle_it12.6385.2682118
X-RAY DIFFRACTIONr_scangle_other12.6355.2682119
X-RAY DIFFRACTIONr_lrange_it1633.47212634
X-RAY DIFFRACTIONr_lrange_other15.99933.47112635
X-RAY DIFFRACTIONr_rigid_bond_restr5.33935229
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
1.51-1.5490.2572700.26849670.26752370.9510.9441000.259
1.549-1.5910.2962870.2547900.25250770.9280.9541000.235
1.591-1.6380.2572100.22347780.22549880.9580.9661000.204
1.638-1.6880.2292770.19445370.19648140.9690.9761000.171
1.688-1.7430.2012290.18744530.18846830.9740.97899.97860.162
1.743-1.8040.1692280.15142660.15244940.980.9871000.128
1.804-1.8720.2062330.1541870.15344200.9780.9881000.127
1.872-1.9480.1932010.15139940.15341950.9750.9881000.129
1.948-2.0340.1782330.14938080.1540410.9790.9891000.131
2.034-2.1330.1741780.14837010.14938790.9770.9891000.131
2.133-2.2480.1791730.12935180.13136910.9780.9911000.117
2.248-2.3830.1771720.12533220.12734940.9840.9921000.116
2.383-2.5470.1651550.12531510.12733060.9850.9911000.119
2.547-2.7490.1771350.1429240.14230590.9790.9881000.137
2.749-3.0090.1641330.14827320.14928650.9840.9861000.149
3.009-3.360.211240.15824450.1625690.9730.9851000.165
3.36-3.8720.1671140.15821920.15923060.9850.9861000.172
3.872-4.7230.1541160.13318590.13419750.9870.991000.154
4.723-6.60.1621020.16414570.16415590.9850.9881000.19
6.6-30.3980.164530.1788880.1779420.9850.98299.89380.203

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