4ow2

YopM from Yersinia enterocolitica WA-314

Method: X-RAY DIFFRACTION Dmax: 130.3 Å Quality: GOOD

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

Yop effector YopM

Yersinia enterocolitica subsp. enterocolitica WA-314

UniProt K1AZR9

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 34–481 Chain C; UniProt 34–481 Fragment:UNP residues 34-481 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;BisTris Propane, sodium citrate, PEG 3350 Resolution 3.20 Å R-free 0.201
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 34–481 Chain D; UniProt 34–481 Fragment:UNP residues 34-481 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;BisTris Propane, sodium citrate, PEG 3350 Resolution 3.20 Å R-free 0.201

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name K1AZR9_YEREN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–448; UniProt 34–481 Author chain B; PDBConstruct 1–448; UniProt 34–481 Author chain C; PDBConstruct 1–448; UniProt 34–481 Author chain D; PDBConstruct 1–448; UniProt 34–481

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 4ow2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4ow2
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id4ow2
Deposition date deposition_date2014-01-30
Structure title titleYopM from Yersinia enterocolitica WA-314
Keywords keywordsleucine-rich repeat, LRR, TOXIN; TOXIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier42.03
Radius of gyration Rg (electron density) rg_electron41.52
Forward intensity I(0) i0585971000.00
Molecular weight molecular_weight200980.0 kDa
Excluded volume excluded_volume252940 ų
Envelope volume envelope_volume369240 ų
Hydration-shell volume shell_volume72993 ų
Envelope diameter envelope_diameter138.2
Shell Rg shell_rg48.53
Envelope Rg envelope_rg39.85
Shape Rg shape_rg41.53
Total Rg total_rg41.88
Total atoms total_atoms14167
Residues n_residues1792
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 dmax130.3
Rg (real space) rg_real41.81
Rg uncertainty (real space) rg_real_error0.93
I(0) (real space) i0_real5.8600e+08
I(0) uncertainty (real space) i0_real_error1.0020e+07
Rg (reciprocal space) rg_reciprocal42.03
I(0) (reciprocal space) i0_reciprocal586100000.0000
Solution quality estimate total_estimate0.8565
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary58.3
Skewness Skewness skewness0.104
Kurtosis Kurtosis kurtosis-0.271
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha84120000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.730

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)