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- PDB-8t27: Crystal Structure of Porphyromonas gingivalis Sialidase (PG_0352)... -

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Basic information

Entry
Database: PDB / ID: 8t27
TitleCrystal Structure of Porphyromonas gingivalis Sialidase (PG_0352) D219A mutant bound to 6'-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 / 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: 1.41 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)57,91910
Polymers56,4941
Non-polymers1,4249
Water8,431468
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.717, 56.791, 80.137
Angle α, β, γ (deg.)90.000, 96.330, 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, 4 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
#6: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3 / 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 , 4 types, 473 molecules

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


Mass: 106.120 Da / Num. of mol.: 2 / 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
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.47 Å3/Da / Density % sol: 50.22 %
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: 1.41→41.67 Å / Num. obs: 103559 / % possible obs: 97.56 % / Redundancy: 3 % / Biso Wilson estimate: 16.26 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.07685 / Rpim(I) all: 0.05282 / Rrim(I) all: 0.09363 / Net I/σ(I): 11.96
Reflection shellResolution: 1.41→1.461 Å / Redundancy: 3 % / Rmerge(I) obs: 0.9888 / Mean I/σ(I) obs: 1.04 / Num. unique obs: 10087 / CC1/2: 0.372 / CC star: 0.737 / Rpim(I) all: 0.6683 / Rrim(I) all: 1.198 / % possible all: 95.23

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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
JBluIce-EPICSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8FEB

8feb


Resolution: 1.41→41.67 Å / SU ML: 0.1587 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.4804
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1801 5276 5.1 %
Rwork0.1561 98201 -
obs0.1574 103477 97.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.59 Å2
Refinement stepCycle: LAST / Resolution: 1.41→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3882 0 95 468 4445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01474423
X-RAY DIFFRACTIONf_angle_d1.46326032
X-RAY DIFFRACTIONf_chiral_restr0.1284647
X-RAY DIFFRACTIONf_plane_restr0.0139808
X-RAY DIFFRACTIONf_dihedral_angle_d7.8057664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.430.27781760.33158X-RAY DIFFRACTION94.21
1.43-1.440.2891710.27743186X-RAY DIFFRACTION95.89
1.44-1.460.27831820.2613189X-RAY DIFFRACTION95.6
1.46-1.480.28571710.24743208X-RAY DIFFRACTION96.16
1.48-1.50.25731690.2353219X-RAY DIFFRACTION95.6
1.5-1.520.2541540.22413186X-RAY DIFFRACTION96.34
1.52-1.540.23311650.20723267X-RAY DIFFRACTION96.16
1.54-1.560.23561530.20173225X-RAY DIFFRACTION96.93
1.56-1.590.21171620.19613254X-RAY DIFFRACTION96.63
1.59-1.620.21811670.19133215X-RAY DIFFRACTION96.71
1.62-1.640.22561900.18513207X-RAY DIFFRACTION96.73
1.64-1.670.20831600.18273292X-RAY DIFFRACTION97.16
1.67-1.70.22511750.18243214X-RAY DIFFRACTION97.3
1.7-1.740.20221670.18893289X-RAY DIFFRACTION97.77
1.74-1.780.20091940.17863265X-RAY DIFFRACTION97.52
1.78-1.820.19451790.16473264X-RAY DIFFRACTION97.81
1.82-1.860.18761520.15743292X-RAY DIFFRACTION97.92
1.86-1.910.14991690.14563284X-RAY DIFFRACTION97.79
1.91-1.970.17582000.14143248X-RAY DIFFRACTION98.15
1.97-2.030.16031590.14353319X-RAY DIFFRACTION97.94
2.03-2.110.17561850.14683245X-RAY DIFFRACTION97.64
2.11-2.190.17611740.14673321X-RAY DIFFRACTION98.42
2.19-2.290.18321800.14093304X-RAY DIFFRACTION98.56
2.29-2.410.16581990.14253281X-RAY DIFFRACTION98.84
2.41-2.560.16551780.14533350X-RAY DIFFRACTION99.16
2.56-2.760.18561840.15263328X-RAY DIFFRACTION99.29
2.76-3.040.1891670.14973365X-RAY DIFFRACTION99.46
3.04-3.480.1651850.14463397X-RAY DIFFRACTION99.69
3.48-4.380.14871890.12673391X-RAY DIFFRACTION99.86
4.38-41.670.15582200.1463438X-RAY DIFFRACTION99.67
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)
11.736317742130.5921688981630.4375362625291.349174622030.3149078130230.944243369949-0.1381503079320.269991471880.101000851928-0.1886209085130.05114624920590.166475758901-0.0558694553817-0.1124793981190.08747226302820.2071949848910.0336774043067-0.0323584877410.239882424380.01166951888090.240658003829-3.979568605057.8636500611814.6086308905
23.81735505327-1.153344470181.07803480241.77286526219-0.6993099021771.29363868046-0.00546101414329-0.02312073704470.2644369913630.0752090008498-0.00966727910717-0.0702904430596-0.0998036539237-0.08842581694250.02166501150110.1277353718570.02684178126670.001698678352610.1277432365650.01097346360160.172507370643-0.16039195320416.723905824918.2553351151
33.09606643855-0.823894357050.3893021592340.485716706002-0.2647647889920.5791443853530.0458745002758-0.142757318308-0.059811337815-0.01712313608490.0534880077630.138457774139-0.0215780975615-0.12056852106-0.1077147936380.142540242148-0.000391232318161-0.007117889266080.1121966613390.02065062828350.1890072140130.9245720626439.1253779136819.5295773759
41.114774657940.2444866709750.4038991571641.199356155620.5062426560142.501886850430.00108645893237-0.01457691330450.073315834036-0.06480671013870.0295829440269-0.0275274577917-0.086140180792-0.0104497726283-0.02919880427170.1085345400340.002015718912380.005577749462180.1086644028750.008456578216060.13098921824827.26718780652.4726579107312.0664941864
50.6932875845780.03039531786440.07010585731880.9100364050110.411536019341.088060721630.0148933019670.00415971499559-0.0209943315685-0.0252615347532-0.00153451261651-0.07078620905090.04584420767370.0801223088857-0.01907003005920.1002805304980.0103231913682-0.003566469440930.118658521722-0.0008697600644430.12370006420736.6120216422-12.600647425314.5847108578
62.639686673650.0937046992649-0.1333272590071.03794838071-0.0785302525040.998259010293-0.0316382674108-0.0684600587766-0.1796232134290.07008582200490.02394741830090.03077274367170.1205269029650.01039980213110.0001167385928410.1471773215330.00362378327115-0.008091776620620.1051665796130.005287348276020.12827845936827.4953964462-19.351626593626.1989873506
70.766297676852-0.301801537563-0.1194422175021.95825971735-0.760225538331.82094354230.00785134612402-0.0773084356703-0.01399210876440.1975960683590.0293155833490.0975853710812-0.0209590843653-0.0308899955212-0.03501282918010.1012024998610.002619946833480.01164190624810.129330337471-0.002521441576540.1108661662717.0869060126-4.7404967453430.3979287097
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 257 )190 - 257171 - 238
55chain 'A' and (resid 258 through 363 )258 - 363239 - 344
66chain 'A' and (resid 364 through 436 )364 - 436345 - 417
77chain 'A' and (resid 437 through 523 )437 - 523418 - 504

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