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- PDB-10qh: Crystal Structure of Treponema denticola Sialidase (TDE_0471) Bou... -

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Basic information

Entry
Database: PDB / ID: 10qh
TitleCrystal Structure of Treponema denticola Sialidase (TDE_0471) Bound to Neu5Ac (NANA)
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 / TRIETHYLENE GLYCOL / N-acetyl-beta-neuraminic acid / exo-alpha-sialidase
Similarity search - Component
Biological speciesTreponema denticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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

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Assembly

Deposited unit
A: exo-alpha-sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,84030
Polymers58,8051
Non-polymers3,03529
Water8,971498
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)129.734, 65.371, 92.021
Angle α, β, γ (deg.)90.00, 106.19, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1135-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein exo-alpha-sialidase


Mass: 58804.672 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
#3: Sugar ChemComp-SLB / N-acetyl-beta-neuraminic acid / N-acetylneuraminic acid / sialic acid / O-sialic acid / 5-N-ACETYL-BETA-D-NEURAMINIC ACID / BETA-SIALIC ACID


Type: D-saccharide, beta linking / Mass: 309.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-neuraminic acidCOMMON NAMEGMML 1.0
b-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 526 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cd
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.19 Å3/Da / Density % sol: 61.4 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 100 mM Tris, pH 8.2, 20 mM Cadmium chloride, 25% PEG400, soak in mother liquor with 15 mM Neu5Ac

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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: 1.56→57.95 Å / Num. obs: 102901 / % possible obs: 97.3 % / Redundancy: 4.6 % / Biso Wilson estimate: 12.28 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.2
Reflection shellResolution: 1.56→1.6 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 3 / Num. unique obs: 4741 / CC1/2: 0.912 / CC star: 0.977 / % possible all: 90.2

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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: 1.56→57.95 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.803 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.15848 5155 5 %RANDOM
Rwork0.14184 ---
obs0.14267 97730 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.6 Å2-0 Å2-0.24 Å2
2--0.46 Å2-0 Å2
3---1.1 Å2
Refinement stepCycle: 1 / Resolution: 1.56→57.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3915 0 91 498 4504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0124469
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163904
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.6595999
X-RAY DIFFRACTIONr_angle_other_deg0.5781.5799050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6075562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.759523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7810669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025318
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021050
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1271.1242164
X-RAY DIFFRACTIONr_mcbond_other1.1271.1242164
X-RAY DIFFRACTIONr_mcangle_it1.6882.0182754
X-RAY DIFFRACTIONr_mcangle_other1.6892.0192755
X-RAY DIFFRACTIONr_scbond_it3.0951.5252305
X-RAY DIFFRACTIONr_scbond_other3.0951.5272306
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1152.3743246
X-RAY DIFFRACTIONr_long_range_B_refined5.46613.34856
X-RAY DIFFRACTIONr_long_range_B_other5.25712.224737
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.56→1.598 Å
RfactorNum. reflection% reflection
Rfree0.229 395 -
Rwork0.209 6897 -
obs--93.79 %
Refinement TLS params.Method: refined / Origin x: -19.781 Å / Origin y: 33.255 Å / Origin z: 15.243 Å
111213212223313233
T0.0159 Å20.0092 Å20.0041 Å2-0.0359 Å20.0036 Å2--0.0081 Å2
L0.7829 °2-0.0165 °20.2489 °2-0.6668 °20.149 °2--0.9285 °2
S-0.0357 Å °-0.1666 Å °-0.0096 Å °0.0913 Å °0.0159 Å °0.042 Å °-0.026 Å °-0.0551 Å °0.0197 Å °

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