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3ee1

Novel fold of VirA, a type III secretion system effector protein from Shigella flexneri

Method: X-RAY DIFFRACTION Dmax: 98.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Effector protein virA

Shigella flexneri

UniProt Q7BU69

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 14–400 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.01 Å R-free 0.256
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 14–400 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.01 Å R-free 0.256

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 3EE1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3EB8 VirA Deposited 2008-08-27 Different construct Different mutation/modification Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 45–400（356 aa） Fragment：delta44
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å R-free 0.267
3EB8 VirA Deposited 2008-08-27 Different construct Different mutation/modification Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 45–400（356 aa） Fragment：delta44
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å R-free 0.267
3EB8 VirA Deposited 2008-08-27 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 45–400（356 aa） Fragment：delta44
Chain B 45–400（356 aa） Fragment：delta44
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å R-free 0.267
4FMB VirA-Rab1 complex structure Deposited 2012-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 45–400（356 aa）
Not recorded AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；298 K；0.8 M ammonium sulfate and 0.1 M Tris-HCl (pH 7.6), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.247
4FMB VirA-Rab1 complex structure Deposited 2012-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 45–400（356 aa）
Not recorded AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；298 K；0.8 M ammonium sulfate and 0.1 M Tris-HCl (pH 7.6), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.247
4FMB VirA-Rab1 complex structure Deposited 2012-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 45–400（356 aa）
Not recorded AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；298 K；0.8 M ammonium sulfate and 0.1 M Tris-HCl (pH 7.6), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.247
4FMB VirA-Rab1 complex structure Deposited 2012-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 45–400（356 aa）
Chain C 45–400（356 aa）
Chain E 45–400（356 aa）
Not recorded AF3 ALUMINUM FLUORIDE × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；298 K；0.8 M ammonium sulfate and 0.1 M Tris-HCl (pH 7.6), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.247

2 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VIRA_SHIFL
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 14–400； UniProt 14–400 Author chain B； PDBConstruct 14–400； UniProt 14–400

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 3ee1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3ee1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3ee1
Deposition date deposition_date2008-09-03
Structure title titleNovel fold of VirA, a type III secretion system effector protein from Shigella flexneri
Keywords keywordsbeta barrels, six-stranded beta barrel, Hydrolase, Protease, Secreted, Thiol protease, Virulence; HYDROLASE
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_guinier30.08 Å
Radius of gyration Rg (electron density) rg_electron29.64 Å
Forward intensity I(0) i092615600.00
Molecular weight molecular_weight74945.0 kDa
Excluded volume excluded_volume93206 ų
Envelope volume envelope_volume121200 ų
Hydration-shell volume shell_volume35047 ų
Envelope diameter envelope_diameter106.3 Å
Shell Rg shell_rg35.96 Å
Envelope Rg envelope_rg29.62 Å
Shape Rg shape_rg29.64 Å
Total Rg total_rg30.25 Å
Total atoms total_atoms5244
Residues n_residues672
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 dmax98.5 Å
Rg (real space) rg_real30.10 Å
Rg uncertainty (real space) rg_real_error0.56 Å
I(0) (real space) i0_real9.2620e+07
I(0) uncertainty (real space) i0_real_error1.4180e+06
Rg (reciprocal space) rg_reciprocal30.09 Å
I(0) (reciprocal space) i0_reciprocal92610000.0000
Solution quality estimate total_estimate0.8871
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary35.3 Å
Skewness Skewness skewness0.375
Kurtosis Kurtosis kurtosis-0.324
Angular range angular_range— – 0.2650 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha19390000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.866
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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) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3ee1A01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily460 — EspG protein, N-terminal domain
Domain ID domain_id3ee1B01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily460 — EspG protein, N-terminal domain
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8. Citations (1)

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9. Files and Curves (10)