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- PDB-8f70: Identification of an Immunodominant region on a Group A Streptoco... -

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Basic information

Entry
Database: PDB / ID: 8f70
TitleIdentification of an Immunodominant region on a Group A Streptococcus T-antigen Reveals Temperature-Dependent Motion in Pili
ComponentsT18.1 Major pilin backbone protein T-antigen,Major pilin backbone protein T-antigen
KeywordsSTRUCTURAL PROTEIN / Streptococcus T-antigen major pilin backbone protein
Function / homology
Function and homology information


Immunoglobulin-like - #3050 / Streptococcal pilin isopeptide linker / Spy0128-like isopeptide containing domain / Streptococcal pilin isopeptide linker superfamily / : / Domain of unknown function (DUF7601) / Collagen-binding surface protein Cna, B-type domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major pilin backbone protein T-antigen
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsYoung, P.G. / Moreland, N.J.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Other government New Zealand
CitationJournal: Virulence / Year: 2023
Title: Identification of an immunodominant region on a group A Streptococcus T-antigen reveals temperature-dependent motion in pili.
Authors: Raynes, J.M. / Young, P.G. / Lorenz, N. / Loh, J.M.S. / McGregor, R. / Baker, E.N. / Proft, T. / Moreland, N.J.
History
DepositionNov 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T18.1 Major pilin backbone protein T-antigen,Major pilin backbone protein T-antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4063
Polymers62,3261
Non-polymers802
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: The assembly is identical to the non-covalently linked T1 antigen crystal packing
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.294, 46.976, 380.633
Angle α, β, γ (deg.)90.00, 90.12, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein T18.1 Major pilin backbone protein T-antigen,Major pilin backbone protein T-antigen


Mass: 62326.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: tee / Plasmid: pProExHta / Production host: Escherichia coli (E. coli) / References: UniProt: A0A096ZH83
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.12M 1,6-Hexanediol, 0.12M 1-Butanol, 0.12M 1,2-Propanediol, 0.12M 2-Propanol, 0.12M 1,4-Butanediol, 0.12M 1,3-Propanediol, 0.1M Sodium HEPES, 0.1M MOPS (acid), 20% v/v Ethylene glycol, 10 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.29→47.58 Å / Num. obs: 27529 / % possible obs: 99.4 % / Redundancy: 5.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.071 / Rrim(I) all: 0.17 / Χ2: 0.94 / Net I/σ(I): 7.2 / Num. measured all: 145410
Reflection shellResolution: 2.29→2.37 Å / % possible obs: 95 % / Redundancy: 5.2 % / Rmerge(I) obs: 1.09 / Num. measured all: 13215 / Num. unique obs: 2540 / CC1/2: 0.714 / Rpim(I) all: 0.506 / Rrim(I) all: 1.206 / Χ2: 1 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
XDSVERSION Jun 1, 2017data reduction
Aimless1.17.29data scaling
PHASER2.8.2phasing
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6N0A

6n0a


Resolution: 2.29→47.58 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.911 / SU B: 8.434 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.33 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25366 1357 4.9 %RANDOM
Rwork0.18945 ---
obs0.19261 26169 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.739 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å2-0 Å2-0.24 Å2
2--1.2 Å2-0 Å2
3----3.49 Å2
Refinement stepCycle: 1 / Resolution: 2.29→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4303 0 2 213 4518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134379
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174021
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.6555932
X-RAY DIFFRACTIONr_angle_other_deg1.221.5929315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5545566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21525.464194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63415737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.337158
X-RAY DIFFRACTIONr_chiral_restr0.0550.2597
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025007
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02913
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8213.8372267
X-RAY DIFFRACTIONr_mcbond_other2.8153.8362266
X-RAY DIFFRACTIONr_mcangle_it4.3625.7492832
X-RAY DIFFRACTIONr_mcangle_other4.3635.752833
X-RAY DIFFRACTIONr_scbond_it3.4694.12112
X-RAY DIFFRACTIONr_scbond_other3.4644.0972109
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5935.9963099
X-RAY DIFFRACTIONr_long_range_B_refined7.28242.2294294
X-RAY DIFFRACTIONr_long_range_B_other7.25342.1464260
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.35 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 97 -
Rwork0.282 1767 -
obs--93.11 %

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