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

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Basic information

Entry
Database: PDB / ID: 8feb
TitleCrystal Structure of Porphyromonas gingivalis Sialidase (PG_0352)
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 / intracellular membrane-bounded organelle / membrane / cytoplasm
Similarity search - Function
BNR repeat-like domain / Sialidase family / Sialidase / Sialidase superfamily
Similarity search - Domain/homology
CITRATE ANION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / exo-alpha-sialidase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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
DepositionDec 6, 2022Deposition 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)57,1785
Polymers56,5381
Non-polymers6404
Water8,215456
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.629, 56.818, 79.976
Angle α, β, γ (deg.)90.000, 96.130, 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 , 1 types, 1 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

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Non-polymers , 5 types, 460 molecules

#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


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


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8 M Ammonium citrate tribasic

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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 PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.84→46.23 Å / Num. obs: 47211 / % possible obs: 98.42 % / Redundancy: 3.8 % / Biso Wilson estimate: 13.87 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.08266 / Rpim(I) all: 0.04909 / Rrim(I) all: 0.09651 / Net I/σ(I): 10.67
Reflection shellResolution: 1.84→1.906 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.3557 / Mean I/σ(I) obs: 3.52 / Num. unique obs: 4717 / CC1/2: 0.89 / CC star: 0.97 / Rpim(I) all: 0.2124 / Rrim(I) all: 0.4157 / % possible all: 98.5

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Processing

Software
NameVersionClassification
xia2XIA2 3.8.0-g3d570883-tags-v3.8.0-0data reduction
DIALSDIALS 3.8.0-gdc8ae182e-releasedata reduction
PHENIX1.2.0.1-4487phasing
Coot0.9.8.5model building
PHENIX1.2.0.1-4487refinement
Aimless0.7.9data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→46.23 Å / SU ML: 0.1719 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.0793
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1888 4555 5.08 %
Rwork0.1557 85193 -
obs0.1574 47199 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.56 Å2
Refinement stepCycle: LAST / Resolution: 1.84→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3858 0 43 456 4357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00754222
X-RAY DIFFRACTIONf_angle_d0.9255754
X-RAY DIFFRACTIONf_chiral_restr0.0634607
X-RAY DIFFRACTIONf_plane_restr0.0093781
X-RAY DIFFRACTIONf_dihedral_angle_d10.3003627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.860.26931800.23332649X-RAY DIFFRACTION88.63
1.86-1.880.23051330.21562763X-RAY DIFFRACTION93.84
1.88-1.90.23151460.20342855X-RAY DIFFRACTION94.64
1.9-1.930.21751290.19252823X-RAY DIFFRACTION95.32
1.93-1.950.23031540.19442859X-RAY DIFFRACTION95.44
1.95-1.980.20921630.18552794X-RAY DIFFRACTION95.76
1.98-2.010.22611440.1912823X-RAY DIFFRACTION95.22
2.01-2.040.27451660.17992866X-RAY DIFFRACTION95.53
2.04-2.070.20361430.17342826X-RAY DIFFRACTION95.81
2.07-2.10.21991350.16782855X-RAY DIFFRACTION94.35
2.1-2.140.23711440.17192814X-RAY DIFFRACTION95.24
2.14-2.180.19961430.16732810X-RAY DIFFRACTION93.98
2.18-2.220.20791360.15762793X-RAY DIFFRACTION92.9
2.22-2.270.21211320.15652675X-RAY DIFFRACTION89.39
2.27-2.320.19751490.15572775X-RAY DIFFRACTION95.37
2.32-2.370.18341740.15532879X-RAY DIFFRACTION96.55
2.37-2.430.19851490.15732894X-RAY DIFFRACTION97.81
2.43-2.490.20761440.15822873X-RAY DIFFRACTION96.7
2.49-2.570.22241520.16462918X-RAY DIFFRACTION96.94
2.57-2.650.23311730.16062885X-RAY DIFFRACTION97.2
2.65-2.750.19641370.16152837X-RAY DIFFRACTION96.46
2.75-2.860.16271620.15272868X-RAY DIFFRACTION95.92
2.86-2.980.18861730.15292843X-RAY DIFFRACTION96.48
2.99-3.140.17521440.15142850X-RAY DIFFRACTION95.93
3.14-3.340.181460.14932804X-RAY DIFFRACTION93.3
3.34-3.60.16251600.13352897X-RAY DIFFRACTION98.61
3.6-3.960.1461640.12482954X-RAY DIFFRACTION99.05
3.96-4.530.14441800.11542869X-RAY DIFFRACTION98.74
4.53-5.710.13461520.12812974X-RAY DIFFRACTION98.49
5.71-46.230.20921480.17452868X-RAY DIFFRACTION96.42
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)
12.85030888102-0.7630881931930.2632023536791.29116121293-0.473236976920.7642416982280.0189730478731-0.03071300623690.1362427442970.03164721686860.04212723514650.132468542283-0.0751919033319-0.186096672915-0.03594743997920.1387394098270.03353710020870.01157085607760.126612833790.01532121977060.127870419732-0.92765016411914.518508367917.8671657186
20.808932018421-0.119415601656-0.2069146757710.771005807389-0.07081721912490.8459745014590.0023876681367-0.0543180639377-0.0283803821460.04856598901520.0120687576698-0.01439226330030.04084644606950.0286958192874-0.01272115762610.0812226122315-0.00414850653558-0.01086196732220.0714632904113-0.003638747301480.045302117729327.7042086721-8.6948402798420.745420537
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 23 through 189 )23 - 1891 - 167
22chain 'A' and (resid 190 through 523 )190 - 523168 - 501

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