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- PDB-10qf: Crystal Structure of Treponema denticola Sialidase (TDE_0471) -

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Basic information

Entry
Database: PDB / ID: 10qf
TitleCrystal Structure of Treponema denticola Sialidase (TDE_0471)
Componentsexo-alpha-sialidase
KeywordsHYDROLASE / sialidase / neuraminidase / virulence factor
Function / homology
Function and homology information


ganglioside catabolic process / cell envelope / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / membrane / cytoplasm
Similarity search - Function
Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / BNR repeat-like domain / Sialidase family / Sialidase / Sialidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
: / CITRIC ACID / TRIETHYLENE GLYCOL / exo-alpha-sialidase
Similarity search - Component
Biological speciesTreponema denticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.627 Å
AuthorsClark, N.D. / Malkowski, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01DE023080 United States
CitationJournal: Biorxiv / Year: 2026
Title: Bacterial exo-alpha-sialidases subvert the complement system through desialylation.
Authors: Kurniyati, K. / Clark, N.D. / Fu, Q. / Zhang, S. / Qiu, W. / Malkowski, M.G. / Li, C.
History
DepositionFeb 1, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: exo-alpha-sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,90234
Polymers58,7891
Non-polymers3,11333
Water8,629479
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.794, 65.479, 92.042
Angle α, β, γ (deg.)90.000, 106.783, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein exo-alpha-sialidase


Mass: 58788.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola (bacteria) / Gene: TDE_0471 / Plasmid: pQE80L / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Lemo21 / References: UniProt: Q73QH2, exo-alpha-sialidase

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Non-polymers , 7 types, 512 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.18 Å3/Da / Density % sol: 61.38 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 25 mM Citric acid, 75 mM Bis-tris propane, pH 7.4, 20 mM Cadmium chloride, 25% PEG400, seeded

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0331 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 1.627→45.71 Å / Num. obs: 88676 / % possible obs: 95.8 % / Redundancy: 2.7 % / Biso Wilson estimate: 12.73 Å2 / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.109 / Net I/σ(I): 5.7
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 2.7 % / Rmerge(I) obs: 1.033 / Mean I/σ(I) obs: 1 / Num. unique obs: 4083 / CC1/2: 0.571 / CC star: 0.853 / % possible all: 88.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Cootmodel building
BUCCANEERmodel building
PHASER2.3.8phasing
Aimless0.7.9data scaling
xia23.8.0data reduction
DIALS3.8.0data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.627→45.709 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.315 / SU ML: 0.06 / Cross valid method: FREE R-VALUE / ESU R: 0.074 / ESU R Free: 0.075
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1869 4601 5.191 %
Rwork0.1638 84039 -
all0.165 --
obs-88640 95.527 %
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: 17.401 Å2
Baniso -1Baniso -2Baniso -3
1--1.579 Å2-0 Å2-0.224 Å2
2--1.476 Å20 Å2
3---0.202 Å2
Refinement stepCycle: LAST / Resolution: 1.627→45.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 0 114 479 4503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0124402
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163912
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.665958
X-RAY DIFFRACTIONr_angle_other_deg0.5611.5799035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3665558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.924523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44410644
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.71110204
X-RAY DIFFRACTIONr_chiral_restr0.080.2633
X-RAY DIFFRACTIONr_chiral_restr_other0.0180.22
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025268
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021053
X-RAY DIFFRACTIONr_nbd_refined0.1980.2741
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.23608
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22065
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.22250
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2399
X-RAY DIFFRACTIONr_metal_ion_refined0.3080.214
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2410.229
X-RAY DIFFRACTIONr_nbd_other0.1510.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.229
X-RAY DIFFRACTIONr_mcbond_it0.9150.932148
X-RAY DIFFRACTIONr_mcbond_other0.9150.9292148
X-RAY DIFFRACTIONr_mcangle_it1.4161.6642734
X-RAY DIFFRACTIONr_mcangle_other1.4221.6652735
X-RAY DIFFRACTIONr_scbond_it2.6011.2622254
X-RAY DIFFRACTIONr_scbond_other2.61.2642255
X-RAY DIFFRACTIONr_scangle_it3.1682.13224
X-RAY DIFFRACTIONr_scangle_other3.1672.1023225
X-RAY DIFFRACTIONr_lrange_it5.90611.1894923
X-RAY DIFFRACTIONr_lrange_other5.74110.4044807
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
1.627-1.6690.3113040.28760000.28968560.9260.93391.94870.292
1.669-1.7150.2793110.26760680.26866380.9430.94696.09820.272
1.715-1.7650.2793410.25558760.25664750.9480.95296.01540.255
1.765-1.8190.2472790.22957460.2362970.960.96295.68050.227
1.819-1.8790.2442880.21251250.21460740.9620.9789.11760.208
1.879-1.9440.2123050.17753110.17958510.9710.97995.98360.173
1.944-2.0180.1832940.16352860.16457300.9780.98397.38220.158
2.018-2.10.1872750.15850240.15954440.9790.98497.33650.152
2.1-2.1930.182740.15548660.15652770.9810.98697.40380.15
2.193-2.30.1752690.14946360.15150350.9790.98797.41810.144
2.3-2.4240.1742550.13644110.13847990.9810.98997.22860.133
2.424-2.570.1612180.13140670.13245000.9840.9995.22220.129
2.57-2.7470.1571890.13536410.13642670.9850.98989.75860.134
2.747-2.9670.1782050.13537360.13739890.9810.98998.79670.138
2.967-3.2480.1722000.14434080.14636500.9820.98898.84930.149
3.248-3.6290.1641810.14831220.14933490.9830.98898.62640.155
3.629-4.1870.1551510.13826950.13929290.9870.98997.16630.151
4.187-5.1170.1271030.11621070.11725000.9920.99388.40.134
5.117-7.1910.1941080.18618300.18719560.9850.98799.07980.2
7.191-45.7090.242510.20910810.2111360.9610.97499.64790.227
Refinement TLS params.Method: refined / Origin x: -19.8947 Å / Origin y: 33.2874 Å / Origin z: 15.1017 Å
111213212223313233
T0.0106 Å20.0051 Å20.0052 Å2-0.0492 Å20.0091 Å2--0.0635 Å2
L0.4004 °20.0396 °20.1167 °2-0.3901 °20.1618 °2--0.9593 °2
S-0.0185 Å °-0.0845 Å °-0.0238 Å °0.0583 Å °0.0013 Å °0.0356 Å °0.0012 Å °-0.0371 Å °0.0172 Å °
Refinement TLS groupSelection: ALL

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