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- PDB-10qg: Crystal Structure of Treponema denticola Sialidase (TDE_0471) bou... -

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Basic information

Entry
Database: PDB / ID: 10qg
TitleCrystal Structure of Treponema denticola Sialidase (TDE_0471) bound to Neu5Ac2en (DANA)
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
: / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / DI(HYDROXYETHYL)ETHER / exo-alpha-sialidase
Similarity search - Component
Biological speciesTreponema denticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.549 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)62,47933
Polymers58,7891
Non-polymers3,69132
Water9,998555
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)129.811, 65.547, 91.679
Angle α, β, γ (deg.)90.000, 106.148, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1109-

HOH

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Components

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Protein / Sugars , 2 types, 3 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
#2: Sugar ChemComp-DAN / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Neu5Ac2en


Type: D-saccharide / Mass: 291.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17NO8 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 4 types, 585 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Cd
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 3.19 Å3/Da / Density % sol: 61.4 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 100 mM HEPES, pH 7.8, 20 mM Cadmium chloride, 25% PEG400, soak in mother liquor with 25 mM DANA for 20 min

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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: 1.549→59.314 Å / Num. obs: 104014 / % possible obs: 97.1 % / Redundancy: 4.7 % / Biso Wilson estimate: 9.5 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.8
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 4956 / CC1/2: 0.943 / CC star: 0.985 / % possible all: 94.6

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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: 1.549→59.314 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.481 / SU ML: 0.032 / Cross valid method: FREE R-VALUE / ESU R: 0.055 / ESU R Free: 0.054
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.153 5239 5.037 %Random
Rwork0.1378 98767 --
all0.139 ---
obs-104006 96.852 %-
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: 14.886 Å2
Baniso -1Baniso -2Baniso -3
1--1.307 Å20 Å2-0.15 Å2
2--0.854 Å20 Å2
3---0.463 Å2
Refinement stepCycle: LAST / Resolution: 1.549→59.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3918 0 97 555 4570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0124507
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163981
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.6586113
X-RAY DIFFRACTIONr_angle_other_deg0.5791.5859209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5885576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.71531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5410678
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg2.029101
X-RAY DIFFRACTIONr_dihedral_angle_6_deg18.09610213
X-RAY DIFFRACTIONr_chiral_restr0.0860.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025466
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021087
X-RAY DIFFRACTIONr_nbd_refined0.2050.2741
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.23632
X-RAY DIFFRACTIONr_nbtor_refined0.180.22062
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.22194
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2386
X-RAY DIFFRACTIONr_metal_ion_refined0.1550.213
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3640.215
X-RAY DIFFRACTIONr_nbd_other0.2740.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.215
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0690.24
X-RAY DIFFRACTIONr_mcbond_it0.9330.9742196
X-RAY DIFFRACTIONr_mcbond_other0.9230.9742196
X-RAY DIFFRACTIONr_mcangle_it1.3831.7522808
X-RAY DIFFRACTIONr_mcangle_other1.3831.7532809
X-RAY DIFFRACTIONr_scbond_it2.0941.1712311
X-RAY DIFFRACTIONr_scbond_other2.0931.1712312
X-RAY DIFFRACTIONr_scangle_it2.5262.0243305
X-RAY DIFFRACTIONr_scangle_other2.5262.0233306
X-RAY DIFFRACTIONr_lrange_it4.65710.7764980
X-RAY DIFFRACTIONr_lrange_other4.42410.1184841
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
1.549-1.5890.2023560.1771470.17178950.9760.98395.03480.161
1.589-1.6330.1874210.15970260.1677060.980.98596.6390.15
1.633-1.680.1583290.14769060.14874750.9840.98796.78930.14
1.68-1.7320.1683230.14267390.14373010.9840.98896.72650.135
1.732-1.7890.1623610.13464530.13670340.9840.98996.87230.129
1.789-1.8510.1413180.1362490.13168090.9880.9996.44590.127
1.851-1.9210.1443240.13257930.13366260.9880.98992.31810.131
1.921-1.9990.1423230.1358760.1363390.9870.9997.79150.13
1.999-2.0880.1483270.13156260.13260790.9870.9997.92730.132
2.088-2.190.172600.13654700.13858390.9840.9998.13320.14
2.19-2.3080.1352670.12451670.12455290.9890.99198.28180.129
2.308-2.4480.1312440.1249230.1252570.9890.99198.2880.127
2.448-2.6170.1582860.12444240.12649640.9850.9994.88320.134
2.617-2.8260.1482210.12341780.12445760.9870.99196.1320.135
2.826-3.0950.1382050.13440190.13442540.9870.98999.29480.151
3.095-3.4590.1391690.14136640.14138560.9890.98999.40350.161
3.459-3.9920.1471940.14531590.14533860.9880.98899.02540.169
3.992-4.8840.1531350.12726890.12829100.9880.99297.04470.156
4.884-6.8830.1791140.17320240.17422510.9880.98994.980.203
6.883-59.3140.183620.20612350.20512990.9820.97199.8460.244
Refinement TLS params.Method: refined / Origin x: -19.7134 Å / Origin y: 33.3232 Å / Origin z: 15.2211 Å
111213212223313233
T0.0121 Å20.0077 Å20.0051 Å2-0.0204 Å20.0023 Å2--0.0028 Å2
L0.454 °20.0146 °20.1016 °2-0.4115 °20.0904 °2--0.698 °2
S-0.0229 Å °-0.0943 Å °-0.0057 Å °0.0621 Å °0.0117 Å °0.0329 Å °-0.0217 Å °-0.0323 Å °0.0111 Å °
Refinement TLS groupSelection: ALL

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