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- PDB-8pvq: Crystal Structure of Human PTX3 C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 8pvq
TitleCrystal Structure of Human PTX3 C-terminal domain
ComponentsPentraxin-related protein PTX3
KeywordsIMMUNE SYSTEM / Binding protein
Function / homology
Function and homology information


(1->3)-beta-D-glucan binding / negative regulation by host of viral glycoprotein metabolic process / negative regulation of glycoprotein metabolic process / ovarian cumulus expansion / negative regulation by host of viral process / opsonization / complement component C1q complex binding / response to yeast / host-mediated suppression of symbiont invasion / virion binding ...(1->3)-beta-D-glucan binding / negative regulation by host of viral glycoprotein metabolic process / negative regulation of glycoprotein metabolic process / ovarian cumulus expansion / negative regulation by host of viral process / opsonization / complement component C1q complex binding / response to yeast / host-mediated suppression of symbiont invasion / virion binding / positive regulation of phagocytosis / extracellular matrix organization / extracellular matrix / specific granule lumen / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / inflammatory response / innate immune response / Neutrophil degranulation / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Pentraxin-related protein PTX3 / LamG-like jellyroll fold / LamG-like jellyroll fold domain / Pentaxin, conserved site / Pentraxin domain signature. / Pentaxin family / Pentraxin / C-reactive protein / pentaxin family / Pentraxin-related / Pentraxin (PTX) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Pentraxin-related protein PTX3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsLevy, C.W.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T001542/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T017643/1 United Kingdom
CitationJournal: To Be Published
Title: Pentraxin 3 mediated crosslinking of heavy chain hyaluronan complexes: new insights from structural and biophysical studies
Authors: Shah, A. / Zhang, X. / Lockhart-Cairns, M.P. / Levy, C.W. / Jowitt, T.A. / Birchenough, H. / Dean, L. / Collins, R. / Dodd, R.J. / Inforzato, A. / Fontana, J. / Baldock, C. / Richter, R.P. / Day, A.J.
History
DepositionJul 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pentraxin-related protein PTX3


Theoretical massNumber of molelcules
Total (without water)22,6111
Polymers22,6111
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.003, 138.003, 69.550
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein Pentraxin-related protein PTX3 / Pentaxin-related protein PTX3 / Tumor necrosis factor alpha-induced protein 5 / TNF alpha-induced ...Pentaxin-related protein PTX3 / Tumor necrosis factor alpha-induced protein 5 / TNF alpha-induced protein 5 / Tumor necrosis factor-inducible gene 14 protein / TSG-14


Mass: 22610.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTX3, TNFAIP5, TSG14 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P26022
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.03 M of each halide, 0.1 M MOPS/HEPES-Na pH 7.5) * 0.3 M sodium fluoride, 0.3 M sodium bromide, 0.3 M sodium iodide
Temp details: Cold room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: May 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.43→45.33 Å / Num. obs: 9663 / % possible obs: 99.54 % / Redundancy: 6.5 % / Biso Wilson estimate: 62.77 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.044 / Net I/σ(I): 8.66
Reflection shellResolution: 2.43→2.517 Å / Mean I/σ(I) obs: 1.08 / Num. unique obs: 950 / CC1/2: 0.892 / Rpim(I) all: 0.66 / % possible all: 99.37

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→45.33 Å / SU ML: 0.307 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.8652
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2623 483 5.01 %
Rwork0.2164 9154 -
obs0.2187 9637 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.94 Å2
Refinement stepCycle: LAST / Resolution: 2.43→45.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 0 21 1567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00881580
X-RAY DIFFRACTIONf_angle_d0.78982142
X-RAY DIFFRACTIONf_chiral_restr0.0546237
X-RAY DIFFRACTIONf_plane_restr0.005274
X-RAY DIFFRACTIONf_dihedral_angle_d5.516212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.780.37271590.30453009X-RAY DIFFRACTION99.28
2.78-3.50.33011610.25453035X-RAY DIFFRACTION99.72
3.5-45.330.22471630.1913110X-RAY DIFFRACTION99.48

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