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- PDB-8c27: Domain 3 of Group B Streptococcus pilus protein as scaffold for t... -

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Basic information

Entry
Database: PDB / ID: 8c27
TitleDomain 3 of Group B Streptococcus pilus protein as scaffold for the display of foreign epitopes
ComponentsPI-2a backbone protein
KeywordsMEMBRANE PROTEIN / Pilus protein / scaffold / epitopes.
Function / homology
Function and homology information


Gram-positive pilin backbone subunit 3, Cna-B-like domain / Gram-positive pilin backbone subunit 3, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin subunit D1, N-terminal / Gram-positive pilin subunit D1, N-terminal domain / Fimbrial isopeptide formation D2 domain / Prealbumin-like fold domain / Prealbumin-like fold domain / LPXTG cell wall anchor motif ...Gram-positive pilin backbone subunit 3, Cna-B-like domain / Gram-positive pilin backbone subunit 3, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin subunit D1, N-terminal / Gram-positive pilin subunit D1, N-terminal domain / Fimbrial isopeptide formation D2 domain / Prealbumin-like fold domain / Prealbumin-like fold domain / LPXTG cell wall anchor motif / LPXTG cell wall anchor domain / Immunoglobulin-like fold
Similarity search - Domain/homology
PI-2a backbone protein
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsVeggi, D. / Cappelli, L. / Cozzi, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Faseb J. / Year: 2024
Title: Computational structure-based approach to study chimeric antigens using a new protein scaffold displaying foreign epitopes.
Authors: Cappelli, L. / Cinelli, P. / Perrotta, A. / Veggi, D. / Audagnotto, M. / Tuscano, G. / Pansegrau, W. / Bartolini, E. / Rinaudo, D. / Cozzi, R.
History
DepositionDec 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PI-2a backbone protein
B: PI-2a backbone protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4574
Polymers29,3332
Non-polymers1242
Water1086
1
A: PI-2a backbone protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7903
Polymers14,6661
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PI-2a backbone protein


Theoretical massNumber of molelcules
Total (without water)14,6661
Polymers14,6661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.391, 118.047, 189.815
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Space group name HallF22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x,y+1/2,z+1/2
#6: x,-y+1/2,-z+1/2
#7: -x,y+1/2,-z+1/2
#8: -x,-y+1/2,z+1/2
#9: x+1/2,y,z+1/2
#10: x+1/2,-y,-z+1/2
#11: -x+1/2,y,-z+1/2
#12: -x+1/2,-y,z+1/2
#13: x+1/2,y+1/2,z
#14: x+1/2,-y+1/2,-z
#15: -x+1/2,y+1/2,-z
#16: -x+1/2,-y+1/2,z

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Components

#1: Protein PI-2a backbone protein


Mass: 14666.284 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B9UR22
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
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: 3.41 Å3/Da / Density % sol: 63.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES with 20% w/v jeff ED-2001 pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.63→94.9 Å / Num. obs: 12062 / % possible obs: 99.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 60.74 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.5
Reflection shellResolution: 2.63→94.9 Å / Num. unique obs: 12062 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XTL

2xtl


Resolution: 2.63→58.15 Å / SU ML: 0.4785 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.1437
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.279 598 4.96 %
Rwork0.2266 11459 -
obs0.2292 12057 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.1 Å2
Refinement stepCycle: LAST / Resolution: 2.63→58.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2009 0 8 7 2024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01052055
X-RAY DIFFRACTIONf_angle_d1.8222785
X-RAY DIFFRACTIONf_chiral_restr0.0927315
X-RAY DIFFRACTIONf_plane_restr0.0198357
X-RAY DIFFRACTIONf_dihedral_angle_d16.3209751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.90.37971480.32512822X-RAY DIFFRACTION99.76
2.9-3.320.35141580.28142818X-RAY DIFFRACTION99.53
3.32-4.180.27311460.21652863X-RAY DIFFRACTION99.87
4.18-58.150.23161460.1962956X-RAY DIFFRACTION99.45

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