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- PDB-6n0a: Structure of the major pilin protein (T-18.1) from Streptococcus ... -

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Basic information

Entry
Database: PDB / ID: 6n0a
TitleStructure of the major pilin protein (T-18.1) from Streptococcus pyogenes serotype MGAS8232
ComponentsMajor pilin backbone protein T-antigen
KeywordsSTRUCTURAL PROTEIN / Major pilin backbone protein / T-antigen / T18.1
Function / homology
Function and homology information


Immunoglobulin-like - #3050 / Streptococcal pilin isopeptide linker / Streptococcal pilin isopeptide linker superfamily / Spy0128-like isopeptide containing domain / Domain of unknown function DUF5979 / Domain of unknown function (DUF5979) / 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 / molecular replacement / Resolution: 1.75 Å
AuthorsYoung, P.G. / Raynes, J.M. / Loh, J.M. / Proft, T. / Baker, E.N. / Moreland, N.J.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Health Research Council (HRC) New Zealand
CitationJournal: Infect.Immun. / Year: 2019
Title: Group AStreptococcusT Antigens Have a Highly Conserved Structure Concealed under a Heterogeneous Surface That Has Implications for Vaccine Design.
Authors: Young, P.G. / Raynes, J.M. / Loh, J.M. / Proft, T. / Baker, E.N. / Moreland, N.J.
History
DepositionNov 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Aug 25, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value
Revision 1.4Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major pilin backbone protein T-antigen
B: Major pilin backbone protein T-antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1574
Polymers62,0772
Non-polymers802
Water6,521362
1
A: Major pilin backbone protein T-antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0792
Polymers31,0381
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Major pilin backbone protein T-antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0792
Polymers31,0381
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.588, 50.683, 67.924
Angle α, β, γ (deg.)103.550, 93.530, 90.030
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 1 - 282 / Label seq-ID: 1 - 282

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Major pilin backbone protein T-antigen


Mass: 31038.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: tee / Plasmid: pProExHta / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 20000, 20% v/v PEG MME 550, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2-Propanediol, 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 0.1 M BICINE/Tris base pH 8.5

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95468 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95468 Å / Relative weight: 1
ReflectionResolution: 1.75→44.83 Å / Num. obs: 51303 / % possible obs: 96.7 % / Redundancy: 3.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.067 / Rrim(I) all: 0.13 / Net I/σ(I): 9.4
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2572 / CC1/2: 0.636 / Rpim(I) all: 0.496 / Rrim(I) all: 0.952 / % possible all: 89.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BBT

6bbt


Resolution: 1.75→40.54 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.886 / SU B: 4.024 / SU ML: 0.126 / SU R Cruickshank DPI: 0.1625 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.152
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2753 2522 4.9 %RANDOM
Rwork0.2332 ---
obs0.2353 48779 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 49.15 Å2 / Biso mean: 16.762 Å2 / Biso min: 8.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20.38 Å20.48 Å2
2---0.85 Å20.75 Å2
3---0.62 Å2
Refinement stepCycle: final / Resolution: 1.75→40.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4206 0 2 362 4570
Biso mean--20.6 19.89 -
Num. residues----553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0144281
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173875
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.6685791
X-RAY DIFFRACTIONr_angle_other_deg0.8871.6599054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8175549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80225.604182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17415734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.154156
X-RAY DIFFRACTIONr_chiral_restr0.0630.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024780
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02786
Refine LS restraints NCS

Ens-ID: 1 / Number: 8188 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.749→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 193 -
Rwork0.322 3332 -
all-3525 -
obs--90.5 %

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