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- PDB-8t26: Crystal Structure of Porphyromonas gingivalis Sialidase (PG_0352)... -

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Basic information

Entry
Database: PDB / ID: 8t26
TitleCrystal Structure of Porphyromonas gingivalis Sialidase (PG_0352) D219A mutant bound to 3'-Sialyllactose (only Neu5Ac visible)
ComponentsSialidase, putative
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
beta-D-galactopyranose / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / N-acetyl-alpha-neuraminic acid / exo-alpha-sialidase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3906
Polymers56,4941
Non-polymers8965
Water8,809489
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.484, 56.829, 80.026
Angle α, β, γ (deg.)90.000, 96.300, 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, putative


Mass: 56494.340 Da / Num. of mol.: 1 / Mutation: D219A
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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Sugars , 2 types, 2 molecules

#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
#5: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 492 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8 M ammonium citrate tribasic, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0333 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: 1.0333 Å / Relative weight: 1
ReflectionResolution: 1.42→46.08 Å / Num. obs: 103256 / % possible obs: 99.78 % / Redundancy: 4.4 % / Biso Wilson estimate: 15.6 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.1183 / Rpim(I) all: 0.06275 / Rrim(I) all: 0.1345 / Net I/σ(I): 8.66
Reflection shellResolution: 1.421→1.472 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.9658 / Mean I/σ(I) obs: 0.85 / Num. unique obs: 10239 / CC1/2: 0.648 / CC star: 0.887 / Rpim(I) all: 0.5106 / Rrim(I) all: 1.096 / % possible all: 98.65

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
PHASERphasing
xia2data scaling
DIALSdata reduction
xia2data reduction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8FEB

8feb


Resolution: 1.42→46.08 Å / SU ML: 0.1779 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.6779
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1876 5321 5.16 %
Rwork0.1628 97760 -
obs0.1641 103081 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.67 Å2
Refinement stepCycle: LAST / Resolution: 1.42→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3892 0 60 489 4441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094465
X-RAY DIFFRACTIONf_angle_d1.10796100
X-RAY DIFFRACTIONf_chiral_restr0.1085640
X-RAY DIFFRACTIONf_plane_restr0.0118831
X-RAY DIFFRACTIONf_dihedral_angle_d9.0704684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.440.33891550.3133172X-RAY DIFFRACTION97.51
1.44-1.450.32791770.29373233X-RAY DIFFRACTION99.19
1.45-1.470.30541850.27183198X-RAY DIFFRACTION99.24
1.47-1.490.25821700.25563255X-RAY DIFFRACTION99.65
1.49-1.510.29991720.24973227X-RAY DIFFRACTION99.79
1.51-1.530.2441980.22873244X-RAY DIFFRACTION99.88
1.53-1.550.26941680.21453212X-RAY DIFFRACTION99.88
1.55-1.580.20031730.20443304X-RAY DIFFRACTION99.86
1.58-1.60.21231770.19483196X-RAY DIFFRACTION99.91
1.6-1.630.21481790.19193247X-RAY DIFFRACTION99.91
1.63-1.650.22161970.18753241X-RAY DIFFRACTION99.91
1.65-1.680.22561760.18593243X-RAY DIFFRACTION99.97
1.68-1.720.21231710.18743294X-RAY DIFFRACTION99.86
1.72-1.750.22521760.17913214X-RAY DIFFRACTION99.94
1.75-1.790.2371920.183278X-RAY DIFFRACTION99.94
1.79-1.830.22131780.17473247X-RAY DIFFRACTION99.85
1.83-1.880.21251540.15983277X-RAY DIFFRACTION99.97
1.88-1.930.17891860.14813242X-RAY DIFFRACTION99.94
1.93-1.990.17521690.14923268X-RAY DIFFRACTION100
1.99-2.050.16031620.15063303X-RAY DIFFRACTION99.83
2.05-2.120.1961800.15073242X-RAY DIFFRACTION100
2.12-2.210.16931730.14873248X-RAY DIFFRACTION99.97
2.21-2.310.15831810.14223270X-RAY DIFFRACTION99.94
2.31-2.430.19351800.1483266X-RAY DIFFRACTION100
2.43-2.580.14741800.14723310X-RAY DIFFRACTION100
2.58-2.780.17431780.15543269X-RAY DIFFRACTION99.86
2.78-3.060.18721680.15763280X-RAY DIFFRACTION99.97
3.06-3.50.17581900.14963284X-RAY DIFFRACTION100
3.5-4.410.1491880.13553319X-RAY DIFFRACTION100
4.41-46.080.17271880.15663377X-RAY DIFFRACTION99.92
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)
11.942721827120.4433030098520.6567371465940.5747991616290.2179238614180.525971579182-0.1834640253740.2368416436270.200193522432-0.116622109970.06467223939250.126836051708-0.123312794233-0.05574128858220.1214406822370.2510192370220.0324506549962-0.02733003043760.2732404303570.01231599722010.271145628809-4.563873398417.797093152214.0758838608
24.01000912779-1.154808606951.128887587971.90671237601-0.6026000238811.0889364932-0.0481100267746-0.09076385225410.2493780630090.1082571842930.0255333410838-0.054072403976-0.0680443126876-0.100139239570.02103707313270.1326352265160.03231629958450.00935998483740.1361912389790.007613767970270.160091214585-0.68580164586516.842561416717.9025916621
33.48282316675-0.8673145159460.4250407666340.489188148785-0.3316990057110.652639365890.0261040585457-0.168009736664-0.09900086681120.003799754000590.07190250042310.140267455481-0.0578305883817-0.163555469234-0.1050164504490.1361907283110.00784151040940.005192996354550.09146376817850.016744222170.1653243632310.5463937297249.2580605495919.6653155817
40.566825576336-0.132137051055-0.01817957273690.7447428034590.02218999381480.8060056562590.01255388473530.005817458506440.00929185183715-0.02782839398440.0134841745727-0.0632056484719-0.003774715710460.0528277746642-0.02565011161010.104344593126-0.004431942393640.007760707736190.119099263863-0.002283523918080.11623343880432.6968417787-6.4332796495513.5743206439
53.440657647280.3195123525410.09157338200611.23719128854-0.05807595107741.201707070690.00654581589769-0.102101237976-0.1985130902720.07427641952490.002270888477510.03349722037690.1436141666330.00763728158328-0.01192481570070.1310910143270.00416883289453-0.0003646916630840.08054083237280.006071101727170.10439143120527.5294331459-19.252977042726.1959423962
61.1961739303-0.3344685316570.1082695972061.91774183119-0.8165488532992.946417226910.0110294707052-0.0857458233021-0.02335687752810.1903305754870.02034178591170.08774325156280.0055684775654-0.0475035265239-0.02855827329710.08855444844170.001848602472070.02302677696530.104804296029-0.00362347836490.094241665992216.8656776804-4.9449392931530.2465434622
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 20 through 48 )20 - 481 - 29
22chain 'A' and (resid 49 through 151 )49 - 15130 - 132
33chain 'A' and (resid 152 through 189 )152 - 189133 - 170
44chain 'A' and (resid 190 through 363 )190 - 363171 - 344
55chain 'A' and (resid 364 through 436 )364 - 436345 - 417
66chain 'A' and (resid 437 through 523 )437 - 523418 - 504

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