4yxa

Complex of SpaO(SPOA1,2 SeMet) and OrgB(APAR)::T4lysozyme fusion protein

Method: X-RAY DIFFRACTION Dmax: 127.7 Å Quality: REASONABLE

1. Protein Identity and Related Structures Protein Identity & Related Structures

Surface presentation of antigens protein SpaO

Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

UniProt P40699

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 145–213 Chain B; UniProt 232–297 Fragment:UNP Residues 145-213 Fragment:UNP Residues 232-297 Non-standard monomer:Yes (specific site not provided by mmCIF) Oxygen-regulated invasion protein OrgB,Endolysin × 1 (P0CL45,P00720) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;SpaO(145-213, SeMet) + SpaO (232-297, SeMet) + OrgB(1-30)::T4 lysozyme (native) was concentrated to 18mg/mL, supplemented with 50mM maltose, and crystallized with 25% PEG3350, 200mM ammonium formate, 100mM sodium acetate pH=5.0. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment. Crystals were cryoprotected in 25% PEG3350, 10% ethylene glycol, 200mM ammonium formate, 100mM sodium acetate pH=5.0, 50mM maltose. Resolution 2.35 Å R-free 0.262
2 Insufficient information Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 145–213 Chain E; UniProt 232–297 Fragment:UNP Residues 145-213 Fragment:UNP Residues 232-297 Non-standard monomer:Yes (specific site not provided by mmCIF) Oxygen-regulated invasion protein OrgB,Endolysin × 1 (P0CL45,P00720) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;SpaO(145-213, SeMet) + SpaO (232-297, SeMet) + OrgB(1-30)::T4 lysozyme (native) was concentrated to 18mg/mL, supplemented with 50mM maltose, and crystallized with 25% PEG3350, 200mM ammonium formate, 100mM sodium acetate pH=5.0. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment. Crystals were cryoprotected in 25% PEG3350, 10% ethylene glycol, 200mM ammonium formate, 100mM sodium acetate pH=5.0, 50mM maltose. Resolution 2.35 Å R-free 0.262

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.

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPAO_SALTY
Isoform
PDB entities 1, 2
Chains and sequence ranges Author chain A; PDBConstruct 5–73; UniProt 145–213 Author chain D; PDBConstruct 5–73; UniProt 145–213 Author chain B; PDBConstruct 5–70; UniProt 232–297 Author chain E; PDBConstruct 5–70; UniProt 232–297

Oxygen-regulated invasion protein OrgB,Endolysin

Enterobacteria phage T4

UniProt P00720

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 2–164 Fragment:UNP Residues 1-30,UNP Residues 1-30 Mutation:D20N, C54T, C97A,D20N, C54T, C97A Surface presentation of antigens protein SpaO × 1 (P40699) Surface presentation of antigens protein SpaO × 1 (P40699) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;SpaO(145-213, SeMet) + SpaO (232-297, SeMet) + OrgB(1-30)::T4 lysozyme (native) was concentrated to 18mg/mL, supplemented with 50mM maltose, and crystallized with 25% PEG3350, 200mM ammonium formate, 100mM sodium acetate pH=5.0. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment. Crystals were cryoprotected in 25% PEG3350, 10% ethylene glycol, 200mM ammonium formate, 100mM sodium acetate pH=5.0, 50mM maltose. Resolution 2.35 Å R-free 0.262
2 Insufficient information Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 2–164 Fragment:UNP Residues 1-30,UNP Residues 1-30 Mutation:D20N, C54T, C97A,D20N, C54T, C97A Surface presentation of antigens protein SpaO × 1 (P40699) Surface presentation of antigens protein SpaO × 1 (P40699) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;SpaO(145-213, SeMet) + SpaO (232-297, SeMet) + OrgB(1-30)::T4 lysozyme (native) was concentrated to 18mg/mL, supplemented with 50mM maltose, and crystallized with 25% PEG3350, 200mM ammonium formate, 100mM sodium acetate pH=5.0. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment. Crystals were cryoprotected in 25% PEG3350, 10% ethylene glycol, 200mM ammonium formate, 100mM sodium acetate pH=5.0, 50mM maltose. Resolution 2.35 Å R-free 0.262

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.

721 other PDB entries and 845 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ENLYS_BPT4
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 35–197; UniProt 2–164 Author chain F; PDBConstruct 35–197; UniProt 2–164

Oxygen-regulated invasion protein OrgB,Endolysin

Enterobacteria phage T4

UniProt P0CL45

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 1–30 Fragment:UNP Residues 1-30,UNP Residues 1-30 Mutation:D20N, C54T, C97A,D20N, C54T, C97A Surface presentation of antigens protein SpaO × 1 (P40699) Surface presentation of antigens protein SpaO × 1 (P40699) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;SpaO(145-213, SeMet) + SpaO (232-297, SeMet) + OrgB(1-30)::T4 lysozyme (native) was concentrated to 18mg/mL, supplemented with 50mM maltose, and crystallized with 25% PEG3350, 200mM ammonium formate, 100mM sodium acetate pH=5.0. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment. Crystals were cryoprotected in 25% PEG3350, 10% ethylene glycol, 200mM ammonium formate, 100mM sodium acetate pH=5.0, 50mM maltose. Resolution 2.35 Å R-free 0.262
2 Insufficient information Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 1–30 Fragment:UNP Residues 1-30,UNP Residues 1-30 Mutation:D20N, C54T, C97A,D20N, C54T, C97A Surface presentation of antigens protein SpaO × 1 (P40699) Surface presentation of antigens protein SpaO × 1 (P40699) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;SpaO(145-213, SeMet) + SpaO (232-297, SeMet) + OrgB(1-30)::T4 lysozyme (native) was concentrated to 18mg/mL, supplemented with 50mM maltose, and crystallized with 25% PEG3350, 200mM ammonium formate, 100mM sodium acetate pH=5.0. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment. Crystals were cryoprotected in 25% PEG3350, 10% ethylene glycol, 200mM ammonium formate, 100mM sodium acetate pH=5.0, 50mM maltose. Resolution 2.35 Å R-free 0.262

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.

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

View Construct and Data Evidence
UniProt name ORGB_SALTY
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 5–34; UniProt 1–30 Author chain F; PDBConstruct 5–34; UniProt 1–30

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 4yxa

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4yxa
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4yxa
Deposition date deposition_date2015-03-22
Structure title titleComplex of SpaO(SPOA1,2 SeMet) and OrgB(APAR)::T4lysozyme fusion protein
Keywords keywordsType III Secretion System, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.33
Radius of gyration Rg (electron density) rg_electron36.44
Forward intensity I(0) i071088800.00
Molecular weight molecular_weight68577.0 kDa
Excluded volume excluded_volume86477 ų
Envelope volume envelope_volume115510 ų
Hydration-shell volume shell_volume29720 ų
Envelope diameter envelope_diameter127.5
Shell Rg shell_rg37.27
Envelope Rg envelope_rg36.29
Shape Rg shape_rg36.48
Total Rg total_rg36.37
Total atoms total_atoms4810
Residues n_residues612
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax127.7
Rg (real space) rg_real38.11
Rg uncertainty (real space) rg_real_error0.53
I(0) (real space) i0_real7.1280e+07
I(0) uncertainty (real space) i0_real_error1.0790e+06
Rg (reciprocal space) rg_reciprocal36.54
I(0) (reciprocal space) i0_reciprocal71070000.0000
Solution quality estimate total_estimate0.5826
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary29.0
Skewness Skewness skewness0.564
Kurtosis Kurtosis kurtosis-0.481
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha2.7090
Highest regularization parameter α highest_alpha7087000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.658; Stabil: 0.916; Sysdev: 0.000; Positv: 1.000; Valcen: 0.407; Smooth: 0.469

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4yxaB00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology330 — Surface presentation of antigens (SPOA)
Homologous superfamily homologous superfamily10 — SpoA-like
Domain ID domain_id4yxaC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40
Domain ID domain_id4yxaE00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology330 — Surface presentation of antigens (SPOA)
Homologous superfamily homologous superfamily10 — SpoA-like
Domain ID domain_id4yxaF00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40

8. Citations (1)

9. Files and Curves (10)