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- PDB-8t24: Crystal Structure of Porphyromonas gingivalis Sialidase (PG_0352)... -

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Basic information

Entry
Database: PDB / ID: 8t24
TitleCrystal Structure of Porphyromonas gingivalis Sialidase (PG_0352)- Fructose bound in CBM
ComponentsSialidase
KeywordsHYDROLASE / sialidase / neuraminidase / carbohydrate binding / virulence factor
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / membrane / cytoplasm
Similarity search - Function
BNR repeat-like domain / Sialidase family / Sialidase / Sialidase superfamily
Similarity search - Domain/homology
CITRATE ANION / D-fructose / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / exo-alpha-sialidase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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)5R01DE023080-10 United States
CitationJournal: Plos Pathog. / Year: 2023
Title: Functional and structural analyses reveal that a dual domain sialidase protects bacteria from complement killing through desialylation of complement factors.
Authors: Clark, N.D. / Pham, C. / Kurniyati, K. / Sze, C.W. / Coleman, L. / Fu, Q. / Zhang, S. / Malkowski, M.G. / Li, C.
History
DepositionJun 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,82710
Polymers56,5381
Non-polymers1,2889
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.418, 55.502, 85.168
Angle α, β, γ (deg.)90.000, 115.090, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Sialidase


Mass: 56538.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: PG_0352 / Plasmid: pQE80L / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q7MX62
#5: Sugar ChemComp-FUD / D-fructose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 4 types, 215 molecules

#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.8 M ammonium citrate tribasic, pH 7.0, 0.1 M D-fructose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.29→69.73 Å / Num. obs: 30701 / % possible obs: 98.91 % / Redundancy: 4.6 % / Biso Wilson estimate: 37.3 Å2 / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.1601 / Rpim(I) all: 0.08486 / Rrim(I) all: 0.1822 / Net I/σ(I): 7.74
Reflection shellResolution: 2.29→2.372 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.8628 / Num. unique obs: 3060 / CC1/2: 0.573 / CC star: 0.854 / Rpim(I) all: 0.473 / Rrim(I) all: 0.9888 / % possible all: 98.73

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Coot0.9.8.7model building
PHASER2.8.2phasing
xia23.8.6data scaling
DIALS3.8data reduction
xia23.8.6data reduction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8FEB

8feb


Resolution: 2.29→69.73 Å / SU ML: 0.2613 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.7569
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2203 1513 4.93 %
Rwork0.1741 29188 -
obs0.1764 30701 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.43 Å2
Refinement stepCycle: LAST / Resolution: 2.29→69.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3806 0 86 207 4099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714025
X-RAY DIFFRACTIONf_angle_d0.95635438
X-RAY DIFFRACTIONf_chiral_restr0.0575581
X-RAY DIFFRACTIONf_plane_restr0.0095720
X-RAY DIFFRACTIONf_dihedral_angle_d11.9222597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.360.26811290.21892557X-RAY DIFFRACTION95.18
2.36-2.440.3121360.23262645X-RAY DIFFRACTION99.29
2.44-2.540.32421070.24032676X-RAY DIFFRACTION99.04
2.54-2.660.23991410.21532538X-RAY DIFFRACTION96.02
2.66-2.80.27481310.20392666X-RAY DIFFRACTION98.76
2.8-2.970.25961380.21072674X-RAY DIFFRACTION99.79
2.97-3.20.24591350.20832659X-RAY DIFFRACTION99.82
3.2-3.520.25831450.17232691X-RAY DIFFRACTION100
3.52-4.030.20691370.15012706X-RAY DIFFRACTION99.82
4.03-5.080.13691700.11862608X-RAY DIFFRACTION97.51
5.08-69.730.2161440.16212768X-RAY DIFFRACTION99.45
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7318919151510.0725678705297-0.1981745501930.2647289238850.04914795072790.2080150521780.0239225228065-0.121929632573-0.179637219934-0.349574001751-0.0825501789085-0.0231507356440.01891038733290.137797572286-0.04636586617670.5268644655110.00669712219430.007460185362320.217348909008-0.03615636623150.2741144571223.55867824072-16.44704659516.77398651141
20.6232010321250.03722274772-0.2510159659530.7334984013090.3216785617170.841171394148-0.0133658774061-0.04560922987910.0291847259941-0.0208699875437-0.02634236131130.00815306052637-0.0058157403657-0.0459516062702-1.98171042472E-50.1731736440480.0111741127816-0.01818954822650.2267262452950.03233921921090.2164793853.308079256294.3622217067636.7339085601
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 31 through 169 )31 - 1691 - 139
22chain 'A' and (resid 170 through 524 )170 - 524140 - 494

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