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- PDB-4p0d: The T6 backbone pilin of serotype M6 Streptococcus pyogenes has a... -

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Basic information

Entry
Database: PDB / ID: 4p0d
TitleThe T6 backbone pilin of serotype M6 Streptococcus pyogenes has a modular three-domain structure decorated with variable loops and extensions
ComponentsTrypsin-resistant surface T6 protein
KeywordsSTRUCTURAL PROTEIN / Ig-like foldIsopeptide bondSortase motifGram-Positive pili
Function / homology
Function and homology information


cell wall / extracellular region
Similarity search - Function
T6 antigen, Ig-like domain / T6 antigen Ig like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Immunoglobulin-like - #740 / : / Prealbumin-like fold domain / Prealbumin-like fold domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...T6 antigen, Ig-like domain / T6 antigen Ig like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Immunoglobulin-like - #740 / : / Prealbumin-like fold domain / Prealbumin-like fold domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Trypsin-resistant surface T6 protein
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsYoung, P.G. / Moreland, N.J. / Loh, J.M. / Bell, A. / Atatoa-Carr, P. / Proft, T. / Baker, E.N.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Health Research Council New Zealand
CitationJournal: Infect.Immun. / Year: 2014
Title: Structural Conservation, Variability, and Immunogenicity of the T6 Backbone Pilin of Serotype M6 Streptococcus pyogenes.
Authors: Young, P.G. / Moreland, N.J. / Loh, J.M. / Bell, A. / Atatoa Carr, P. / Proft, T. / Baker, E.N.
History
DepositionFeb 20, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Jun 5, 2024Group: Advisory / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact ...pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trypsin-resistant surface T6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1095
Polymers52,6881
Non-polymers4214
Water7,945441
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-11 kcal/mol
Surface area21270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.240, 104.240, 84.220
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Trypsin-resistant surface T6 protein / T6 antigen


Mass: 52688.199 Da / Num. of mol.: 1 / Mutation: E292G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M6 (bacteria)
Strain: ATCC BAA-946 / MGAS10394 / Gene: tee6, M6_Spy0160 / Plasmid: pProExHta / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18481
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 2.2 M NaKPO4 pH 6.4, 2 % PEG 400, 0.1 M imidazole, 20 mM Imidazole
PH range: 6.2 - 6.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 20, 2013
RadiationMonochromator: Double Si with sagittaly bent second crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→24.48 Å / Num. obs: 36565 / % possible obs: 89.1 % / Redundancy: 18.2 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.036 / Net I/σ(I): 16.6 / Num. measured all: 665673 / Scaling rejects: 413
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.9-1.9417.40.9393.82766915920.22957.9
8.91-24.4819.10.05144.377334050.01295.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.92 Å19.54 Å
Translation6.92 Å19.54 Å

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Processing

Software
NameVersionClassification
XDS0.2.8data reduction
SCALA2.5.2data scaling
PHASER2.5.2phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
XSCALEdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 4K8W

4k8w


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.356 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2499 1834 5 %RANDOM
Rwork0.209 34549 --
obs0.2111 36383 88.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.37 Å2 / Biso mean: 22.631 Å2 / Biso min: 9.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.25 Å2-0 Å2
2--0.5 Å2-0 Å2
3----1.63 Å2
Refinement stepCycle: final / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 4 441 3917
Biso mean--28.92 31.07 -
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023571
X-RAY DIFFRACTIONr_bond_other_d0.0010.023290
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9584865
X-RAY DIFFRACTIONr_angle_other_deg0.70637595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1335475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33926.111126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.81715566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.819153
X-RAY DIFFRACTIONr_chiral_restr0.0740.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024087
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02740
X-RAY DIFFRACTIONr_mcbond_it1.122.2361902
X-RAY DIFFRACTIONr_mcbond_other1.1152.2351901
X-RAY DIFFRACTIONr_mcangle_it1.8313.3382376
LS refinement shellResolution: 1.9→1.949 Å
RfactorNum. reflection% reflection
Rfree0.479 87 5 %
Rwork0.416 1722 -
obs--59.82 %

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