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7wr2

Cryatal structure of OspC3 C-terminal ankyrin-repeat domain

Method: X-RAY DIFFRACTION Dmax: 56.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

OspC3

Shigella flexneri

UniProt R4X5L7

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 332–484 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG monomethyl ether 550, 0.1 M Bis-Tris propane pH 9.0 Resolution 1.54 Å R-free 0.190

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 7WR2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7WR1 P32 of caspase-4 C258A mutant in complex with OspC3 C-terminal ankyrin-repeat domain Deposited 2022-01-26 Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 332–484（153 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；5% PEG8000, 0.1M Tris-HCl pH 7.5, % 2-propanol
Resolution 2.13 Å R-free 0.200
7WR1 P32 of caspase-4 C258A mutant in complex with OspC3 C-terminal ankyrin-repeat domain Deposited 2022-01-26 Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 332–484（153 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；5% PEG8000, 0.1M Tris-HCl pH 7.5, % 2-propanol
Resolution 2.13 Å R-free 0.200
7WR3 Crystal structure of MBP-fused OspC3 in complex with calmodulin Deposited 2022-01-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 52–484（433 aa）
Not recorded SO4 SULFATE ION × 2 NCA NICOTINAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG3350, 0.1 M Tris pH 8.2-8.4, 0.2 M Lithium Sulfate, 0.7% 1-Butanol
Resolution 1.87 Å R-free 0.228
7WR3 Crystal structure of MBP-fused OspC3 in complex with calmodulin Deposited 2022-01-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 52–484（433 aa）
Not recorded SO4 SULFATE ION × 2 NCA NICOTINAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG3350, 0.1 M Tris pH 8.2-8.4, 0.2 M Lithium Sulfate, 0.7% 1-Butanol
Resolution 1.87 Å R-free 0.228
7WR4 Crystal structure of OspC3-calmodulin-caspase-4 complex Deposited 2022-01-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 53–474（422 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG3350, 0.1 M HEPES pH 7.4, 0.2 M Ammonium sulfate, 0.3 M NDSB-195
Resolution 2.75 Å R-free 0.270
7WR5 Crystal structure of OspC3-calmodulin-caspase-4 complex binding with 2'-aF-NAD+ Deposited 2022-01-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 53–474（422 aa）
Not recorded 5ZV [[(2~{R},3~{R},4~{S},5~{R})-5-(3-aminocarbonylpyridin-1-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG3350, 0.2 M Potassium acetate
Resolution 3.10 Å R-free 0.272

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name R4X5L7_SHIFL
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 9–161； UniProt 332–484

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 7wr2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7wr2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7wr2
Deposition date deposition_date2022-01-26
Structure title titleCryatal structure of OspC3 C-terminal ankyrin-repeat domain
Keywords keywordsADP-riboxanase, effector, ankyrin-repeat domain, TRANSFERASE; TRANSFERASE
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_guinier15.84 Å
Radius of gyration Rg (electron density) rg_electron14.72 Å
Forward intensity I(0) i04566950.00
Molecular weight molecular_weight15523.0 kDa
Excluded volume excluded_volume19564 ų
Envelope volume envelope_volume21663 ų
Hydration-shell volume shell_volume12680 ų
Envelope diameter envelope_diameter57.6 Å
Shell Rg shell_rg20.24 Å
Envelope Rg envelope_rg15.14 Å
Shape Rg shape_rg14.69 Å
Total Rg total_rg15.90 Å
Total atoms total_atoms1088
Residues n_residues136
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 dmax56.3 Å
Rg (real space) rg_real15.80 Å
Rg uncertainty (real space) rg_real_error0.39 Å
I(0) (real space) i0_real4.5670e+06
I(0) uncertainty (real space) i0_real_error5.4510e+04
Rg (reciprocal space) rg_reciprocal15.80 Å
I(0) (reciprocal space) i0_reciprocal4567000.0000
Solution quality estimate total_estimate0.7593
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary50.6 Å
Skewness Skewness skewness0.318
Kurtosis Kurtosis kurtosis-0.119
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1120000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.639; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.953; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)