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2oto

N-terminal fragment of Streptococcus pyogenes M1 protein

Method: X-RAY DIFFRACTION Dmax: 221.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

M protein

Streptococcus pyogenes serotype M1

UniProt Q48WD8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 42–194 Chain B； UniProt 42–194 Fragment：residues 42-194 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；32% MPD, 0.3M ammonium acetate, 0.1M sodium citrate, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 3.04 Å R-free 0.338
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 42–194 Chain D； UniProt 42–194 Fragment：residues 42-194 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；32% MPD, 0.3M ammonium acetate, 0.1M sodium citrate, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 3.04 Å R-free 0.338
3 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 42–194 Chain B； UniProt 42–194 Chain C； UniProt 42–194 Chain D； UniProt 42–194 Fragment：residues 42-194 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；32% MPD, 0.3M ammonium acetate, 0.1M sodium citrate, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 3.04 Å R-free 0.338

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2OTO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2XNX BC1 fragment of streptococcal M1 protein in complex with human fibrinogen Deposited 2010-08-06 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain M 128–263（136 aa） Fragment：BC1 FRAGMENT OF M1, RESIDUES 128-263
Chain N 128–263（136 aa） Fragment：BC1 FRAGMENT OF M1, RESIDUES 128-263
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 16% PEG 3350, 0.2 M SODIUM TARTRATE WITH SEEDS GROWN IN 0.6 M K2/NA2 PO4, 0.12 M (NH4)2SO4, 0.1 M HEPES, PH 7.5
Resolution 3.30 Å R-free 0.325
2XNY A fragment of streptococcal M1 protein in complex with human fibrinogen Deposited 2010-08-06 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain M 42–135（94 aa） Fragment：N-TERMINAL FRAGMENT, RESIDUES 42-134
Chain N 42–135（94 aa） Fragment：N-TERMINAL FRAGMENT, RESIDUES 42-134
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 1.3 M AMMONIUM TARTRATE, 0.1 M MES, PH 6.25.
Resolution 7.50 Å R-free 0.408

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q48WD8_STRP1
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–155； UniProt 42–194 Author chain B； PDBConstruct 3–155； UniProt 42–194 Author chain C； PDBConstruct 3–155； UniProt 42–194 Author chain D； PDBConstruct 3–155； UniProt 42–194

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2oto

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2oto
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2oto
Deposition date deposition_date2007-02-08
Structure title titleN-terminal fragment of Streptococcus pyogenes M1 protein
Keywords keywordshelical coiled coil, fibrinogen-binding, virulence factor, SURFACE ACTIVE PROTEIN, TOXIN; SURFACE ACTIVE PROTEIN, TOXIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier76.53 Å
Radius of gyration Rg (electron density) rg_electron80.03 Å
Forward intensity I(0) i070649700.00
Molecular weight molecular_weight64472.0 kDa
Excluded volume excluded_volume79363 ų
Envelope volume envelope_volume132180 ų
Hydration-shell volume shell_volume23358 ų
Envelope diameter envelope_diameter307.5 Å
Shell Rg shell_rg36.93 Å
Envelope Rg envelope_rg84.08 Å
Shape Rg shape_rg79.80 Å
Total Rg total_rg78.96 Å
Total atoms total_atoms4521
Residues n_residues544
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax221.8 Å
Rg (real space) rg_real72.19 Å
Rg uncertainty (real space) rg_real_error2.22 Å
I(0) (real space) i0_real6.9050e+07
I(0) uncertainty (real space) i0_real_error1.4530e+06
Rg (reciprocal space) rg_reciprocal69.39 Å
I(0) (reciprocal space) i0_reciprocal69400000.0000
Solution quality estimate total_estimate0.6126
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary22.2 Å
Skewness Skewness skewness0.493
Kurtosis Kurtosis kurtosis-0.777
Angular range angular_range— – 0.1000 Å−1
Current regularization parameter α current_alpha0.0183
Highest regularization parameter α highest_alpha3649000.0000
Real-space data points n_real_points21
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.008; Oscil: 0.041; Stabil: 0.951; Sysdev: 1.000; Positv: 1.000; Valcen: 0.082; Smooth: 0.630
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id2otoA00
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily700 —
Domain ID domain_id2otoB00
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily700 —
Domain ID domain_id2otoC00
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily700 —
Domain ID domain_id2otoD00
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily700 —
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8. Citations (1)

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9. Files and Curves (10)