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- PDB-10qi: Crystal Structure of Treponema denticola Sialidase (TDE_0471) D16... -

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Basic information

Entry
Database: PDB / ID: 10qi
TitleCrystal Structure of Treponema denticola Sialidase (TDE_0471) D165A mutant bound to 3'-sialyllactose (only Neu5Ac visible)
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
: / DI(HYDROXYETHYL)ETHER / N-acetyl-alpha-neuraminic acid / exo-alpha-sialidase
Similarity search - Component
Biological speciesTreponema denticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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)60,22614
Polymers58,7451
Non-polymers1,48113
Water8,917495
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)130.445, 66.077, 93.115
Angle α, β, γ (deg.)90.000, 106.620, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1070-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein exo-alpha-sialidase


Mass: 58744.664 Da / Num. of mol.: 1 / Mutation: D165A
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
#2: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 507 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 3.27 Å3/Da / Density % sol: 62.42 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Bis-tris, pH 6.5, 20 mM Cadmium chliride, 23% PEG400, 5 mM 3'-sialyllactose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0331 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 1.81→46.172 Å / Num. obs: 69062 / % possible obs: 99.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 11.5 Å2 / CC1/2: 0.979 / CC star: 0.995 / Rmerge(I) obs: 0.174 / Net I/σ(I): 4.8
Reflection shellResolution: 1.81→1.86 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.108 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4050 / CC1/2: 0.429 / CC star: 0.775 / % possible all: 99.5

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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: 1.81→46.172 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.097 / SU ML: 0.08 / Cross valid method: FREE R-VALUE / ESU R: 0.096 / ESU R Free: 0.093
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1898 3493 5.06 %
Rwork0.1649 65543 -
all0.166 --
obs-69036 99.554 %
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: 16.484 Å2
Baniso -1Baniso -2Baniso -3
1--0.957 Å2-0 Å2-0.464 Å2
2--1.227 Å2-0 Å2
3---0.006 Å2
Refinement stepCycle: LAST / Resolution: 1.81→46.172 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3889 0 59 495 4443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0124268
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163790
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.6625831
X-RAY DIFFRACTIONr_angle_other_deg0.6271.598759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8415546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.716521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96810642
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.45210200
X-RAY DIFFRACTIONr_chiral_restr0.0910.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025227
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021027
X-RAY DIFFRACTIONr_nbd_refined0.1980.2692
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.23552
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22012
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.22178
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2397
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0360.21
X-RAY DIFFRACTIONr_metal_ion_refined0.5020.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2480.218
X-RAY DIFFRACTIONr_nbd_other0.1220.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.219
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0430.22
X-RAY DIFFRACTIONr_mcbond_it1.0050.8492115
X-RAY DIFFRACTIONr_mcbond_other1.0050.8482114
X-RAY DIFFRACTIONr_mcangle_it1.5971.5152684
X-RAY DIFFRACTIONr_mcangle_other1.5971.5162685
X-RAY DIFFRACTIONr_scbond_it2.1531.0232153
X-RAY DIFFRACTIONr_scbond_other2.1521.0252154
X-RAY DIFFRACTIONr_scangle_it2.8361.7863147
X-RAY DIFFRACTIONr_scangle_other2.8351.7883148
X-RAY DIFFRACTIONr_lrange_it5.4619.8634725
X-RAY DIFFRACTIONr_lrange_other5.1968.9624586
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
1.81-1.8570.3082400.29148100.29250860.9240.93499.29220.287
1.857-1.9080.2722350.2647020.2649740.9450.94999.25610.256
1.908-1.9630.232380.2445510.23948040.960.95699.68780.234
1.963-2.0230.2442120.22344880.22447190.9590.96599.59740.215
2.023-2.0890.2372310.21143130.21245570.9620.96899.71470.201
2.089-2.1630.2092110.18941690.1943840.9710.97599.90880.182
2.163-2.2440.1741960.17340520.17342560.980.9899.8120.164
2.244-2.3350.2072570.16138130.16440890.9720.98399.53530.152
2.335-2.4390.192040.15437320.15639490.9760.98599.67080.145
2.439-2.5580.1982060.14434980.14737220.9770.98799.51640.136
2.558-2.6960.1921870.1434130.14336130.9770.98899.64020.133
2.696-2.8580.1571780.13131960.13333770.9830.9999.91120.124
2.858-3.0550.1721630.13630030.13831790.9830.98999.59110.13
3.055-3.2990.1651450.13628420.13729950.9860.9999.73290.132
3.299-3.6120.171410.13925710.1427210.9840.9999.66920.137
3.612-4.0350.1461390.13623350.13624840.9860.9999.59740.136
4.035-4.6530.126970.11320990.11422090.990.99399.41150.115
4.653-5.6840.1751000.12717680.1318730.9860.99399.7330.129
5.684-7.9790.178680.15813860.15914710.9860.98998.84430.159
7.979-46.1720.182450.1898020.1888620.9790.97898.25990.197
Refinement TLS params.Method: refined / Origin x: -19.8543 Å / Origin y: 33.52 Å / Origin z: 14.7503 Å
111213212223313233
T0.0175 Å20.0016 Å2-0.0025 Å2-0.0352 Å20.0112 Å2--0.051 Å2
L0.6104 °2-0.0495 °20.2071 °2-0.8274 °20.1013 °2--0.7409 °2
S-0.0187 Å °-0.0998 Å °-0.0028 Å °0.1118 Å °0.011 Å °0.0389 Å °-0.014 Å °-0.0647 Å °0.0076 Å °
Refinement TLS groupSelection: ALL

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