4yx7

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

Method: X-RAY DIFFRACTION Dmax: 122.7 Å Quality: GOOD

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 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) + SpaO (232-297) + OrgB(1-30)::T4 lysozyme was concentrated to 18.5mg/mL 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 30% PEG3350, 10% glycerol, 200mM ammonium acetate, 100mM sodium acetate pH=5.0. Resolution 2.00 Å R-free 0.210
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 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) + SpaO (232-297) + OrgB(1-30)::T4 lysozyme was concentrated to 18.5mg/mL 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 30% PEG3350, 10% glycerol, 200mM ammonium acetate, 100mM sodium acetate pH=5.0. Resolution 2.00 Å R-free 0.210

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) + SpaO (232-297) + OrgB(1-30)::T4 lysozyme was concentrated to 18.5mg/mL 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 30% PEG3350, 10% glycerol, 200mM ammonium acetate, 100mM sodium acetate pH=5.0. Resolution 2.00 Å R-free 0.210
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) + SpaO (232-297) + OrgB(1-30)::T4 lysozyme was concentrated to 18.5mg/mL 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 30% PEG3350, 10% glycerol, 200mM ammonium acetate, 100mM sodium acetate pH=5.0. Resolution 2.00 Å R-free 0.210

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) + SpaO (232-297) + OrgB(1-30)::T4 lysozyme was concentrated to 18.5mg/mL 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 30% PEG3350, 10% glycerol, 200mM ammonium acetate, 100mM sodium acetate pH=5.0. Resolution 2.00 Å R-free 0.210
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) + SpaO (232-297) + OrgB(1-30)::T4 lysozyme was concentrated to 18.5mg/mL 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 30% PEG3350, 10% glycerol, 200mM ammonium acetate, 100mM sodium acetate pH=5.0. Resolution 2.00 Å R-free 0.210

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 4yx7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4yx7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4yx7
Deposition date deposition_date2015-03-22
Structure title titleComplex of SpaO(SPOA1,2) 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_guinier37.00
Radius of gyration Rg (electron density) rg_electron36.98
Forward intensity I(0) i078718800.00
Molecular weight molecular_weight72510.0 kDa
Excluded volume excluded_volume91630 ų
Envelope volume envelope_volume123310 ų
Hydration-shell volume shell_volume31096 ų
Envelope diameter envelope_diameter129.5
Shell Rg shell_rg37.90
Envelope Rg envelope_rg36.87
Shape Rg shape_rg36.99
Total Rg total_rg37.02
Total atoms total_atoms5104
Residues n_residues654
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 dmax122.7
Rg (real space) rg_real37.53
Rg uncertainty (real space) rg_real_error1.16
I(0) (real space) i0_real7.8720e+07
I(0) uncertainty (real space) i0_real_error1.3200e+06
Rg (reciprocal space) rg_reciprocal37.20
I(0) (reciprocal space) i0_reciprocal78690000.0000
Solution quality estimate total_estimate0.7600
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.4
Skewness Skewness skewness0.555
Kurtosis Kurtosis kurtosis-0.486
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7427000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.730; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.506; Smooth: 0.179

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_id4yx7B00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology330 — Surface presentation of antigens (SPOA)
Homologous superfamily homologous superfamily10 — SpoA-like
Domain ID domain_id4yx7C00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40
Domain ID domain_id4yx7E00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology330 — Surface presentation of antigens (SPOA)
Homologous superfamily homologous superfamily10 — SpoA-like
Domain ID domain_id4yx7F00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40

8. Citations (1)

9. Files and Curves (10)