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- PDB-8t1z: Crystal Structure of Porphyromonas gingivalis Sialidase (PG_0352)... -

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Basic information

Entry
Database: PDB / ID: 8t1z
TitleCrystal Structure of Porphyromonas gingivalis Sialidase (PG_0352) Bound to Neu5Ac (NANA)
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
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: 1.93 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)57,7058
Polymers56,5381
Non-polymers1,1667
Water5,513306
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.255, 56.782, 80.378
Angle α, β, γ (deg.)90.000, 96.070, 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
#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

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Non-polymers , 4 types, 312 molecules

#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 49.97 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.6 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: 1.93→41.53 Å / Num. obs: 40836 / % possible obs: 98.18 % / Redundancy: 3 % / Biso Wilson estimate: 26.69 Å2 / CC1/2: 0.986 / CC star: 0.996 / Rmerge(I) obs: 0.1288 / Rpim(I) all: 0.088 / Rrim(I) all: 0.1566 / Net I/σ(I): 7.52
Reflection shellResolution: 1.93→1.999 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.7913 / Num. unique obs: 3885 / CC1/2: 0.556 / CC star: 0.845 / Rpim(I) all: 0.5471 / Rrim(I) all: 0.9656 / % possible all: 94.43

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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: 1.93→41.53 Å / SU ML: 0.2156 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8837
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2166 2055 5.04 %
Rwork0.1736 38689 -
obs0.1758 40744 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.95 Å2
Refinement stepCycle: LAST / Resolution: 1.93→41.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 78 306 4239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00764198
X-RAY DIFFRACTIONf_angle_d0.99225701
X-RAY DIFFRACTIONf_chiral_restr0.0618609
X-RAY DIFFRACTIONf_plane_restr0.0144759
X-RAY DIFFRACTIONf_dihedral_angle_d11.3606626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.970.30481240.29142391X-RAY DIFFRACTION91.92
1.97-2.020.32021440.26022521X-RAY DIFFRACTION97.33
2.02-2.080.27011380.23412573X-RAY DIFFRACTION97.91
2.08-2.140.25861300.23542571X-RAY DIFFRACTION98
2.14-2.210.27111410.21612543X-RAY DIFFRACTION98.06
2.21-2.290.24011410.19562577X-RAY DIFFRACTION98.23
2.29-2.380.22061290.19232555X-RAY DIFFRACTION98.14
2.38-2.490.25411550.18782544X-RAY DIFFRACTION98.4
2.49-2.620.24571140.18412619X-RAY DIFFRACTION98.84
2.62-2.780.23091300.17992645X-RAY DIFFRACTION99
2.78-30.22941330.17742599X-RAY DIFFRACTION99.09
3-3.30.22921450.16852598X-RAY DIFFRACTION99.2
3.3-3.780.17981520.14852624X-RAY DIFFRACTION99.36
3.78-4.760.1681440.12732632X-RAY DIFFRACTION99.36
4.76-41.530.18711350.1572697X-RAY DIFFRACTION98.92
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)
13.759255197170.5956191454410.4514626461741.104438874420.2768635954280.103439771347-0.1773884323230.5772826909690.299391513512-0.3515840231710.03923590111470.267472896574-0.06063992995230.09671989597450.1378432776270.3851411788370.0204818273449-0.05340251959790.2981266984080.04723602423990.299270637461-3.200010269398.9252666028515.1691845311
25.39683485746-0.7028220306570.5838124748822.856631813880.3188192017930.3659747812320.0013309587175-0.06152898245670.4531400692940.140951740449-0.0198266057952-0.0745039346404-0.0309575681277-0.01364224329540.01449011563320.3079656599110.05219644177070.008372223550110.1980736289940.01695538192790.213268332553-0.3590732735516.904416657818.1554625955
33.08256962992-0.9301047453520.5713644234620.682085444197-0.270692805020.3342642802450.0526702785159-0.139587646964-0.0426372282683-0.01202574058060.03271279211020.105936880012-0.0427763008695-0.172641582763-0.09806689722570.3438305531270.000119656305251-0.008764430393560.2307636251080.01932910006580.2719903016641.082554260119.2708154398919.7245824977
40.854680077458-0.145322963923-0.2399680789291.031441833290.02671539494880.872654780517-0.0217170065263-0.0618754198092-0.01053800064670.01043125966340.02965918212960.001607062081070.04735426240880.0213180328805-0.00635868629320.235438747948-0.00365262232131-0.03060887352050.145989203276-0.0004228929214620.12905113032127.5184492523-8.6976040000820.8866485272
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 22 through 48 )22 - 481 - 27
22chain 'A' and (resid 49 through 151 )49 - 15128 - 130
33chain 'A' and (resid 152 through 189 )152 - 189131 - 168
44chain 'A' and (resid 190 through 523 )190 - 523169 - 502

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