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2ijy

NMR structure ensemble for the reduced DsbA disulphide oxidoreductase from Vibrio Cholerae

Method: SOLUTION NMR Dmax: 51.7 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Thiol:disulfide interchange protein dsbA

Vibrio cholerae

UniProt P32557

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 20–200 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.8；320 K；Ionic strength (raw mmCIF value) 50 mM NaCl；Pressure 1 NMR sample composition：400 uM DsbA U-15N,13C, 10 mM HEPES, 50 mM sodium chloride, ph 6.8, 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition：400 uM DsbA 10%-13C, 10 mM HEPES, 50 mM sodium chloride, ph 6.8, 90% H2O, 10% D2O | 90% H2O/10% D2O Resolution not provided

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 2IJY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BED STRUCTURE OF DISULFIDE OXIDOREDUCTASE Deposited 1996-09-16 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 20–200（181 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；10-13% EG 4K, 0.1M MES, PH 6.0-6.5
Resolution 2.00 Å R-free 0.241
4DVC Structural and functional studies of TcpG, the Vibrio cholerae DsbA disulfide-forming protein required for pilus and cholera toxin production Deposited 2012-02-23 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 19–200（182 aa） Fragment：UNP residues 19-200
Mutation：R134H, V164A DMS DIMETHYL SULFOXIDE × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6.4；277.15 K；PEG 4000, MES, pH 6.4, hanging drop, temperature 277.15K
Resolution 1.20 Å R-free 0.139
7LUI Crystal structure of Vibrio cholerae DsbA in complex with bile salt taurocholate Deposited 2021-02-22 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–200（181 aa）
Not recorded GOL GLYCEROL × 1 TCH TAUROCHOLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris-HCl, pH 8.5, 0.2 M MgCl2, 26-36% PEG4000
Resolution 1.74 Å R-free 0.204

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

View Construct and Data Evidence
UniProt name DSBA_VIBCH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–181； UniProt 20–200

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 2ijy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2ijy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2ijy
Deposition date deposition_date2006-10-02
Structure title titleNMR structure ensemble for the reduced DsbA disulphide oxidoreductase from Vibrio Cholerae
Keywords keywordsthioredoxin domain, helical domain insert, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.08 Å
Radius of gyration Rg (electron density) rg_electron16.87 Å
Forward intensity I(0) i02703670000.00
Molecular weight molecular_weight450350.0 kDa
Excluded volume excluded_volume565570 ų
Envelope volume envelope_volume38467 ų
Hydration-shell volume shell_volume17872 ų
Envelope diameter envelope_diameter60.2 Å
Shell Rg shell_rg24.20 Å
Envelope Rg envelope_rg18.39 Å
Shape Rg shape_rg16.86 Å
Total Rg total_rg17.01 Å
Total atoms total_atoms62876
Residues n_residues3982
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 dmax51.7 Å
Rg (real space) rg_real17.07 Å
Rg uncertainty (real space) rg_real_error0.28 Å
I(0) (real space) i0_real2.7040e+09
I(0) uncertainty (real space) i0_real_error3.0690e+07
Rg (reciprocal space) rg_reciprocal17.07 Å
I(0) (reciprocal space) i0_reciprocal2704000000.0000
Solution quality estimate total_estimate0.9051
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.7 Å
Skewness Skewness skewness0.311
Kurtosis Kurtosis kurtosis-0.403
Angular range angular_range— – 0.4650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha775900.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.956
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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

SCOP 2.08 (1 domains)

Domain ID domain_idd2ijya_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.47 — Thioredoxin fold
Superfamily Superfamily superfamilyc.47.1 — Thioredoxin-like
Family Family familyc.47.1.13 — DsbA-like

CATH v4.4 (1 domains)

Domain ID domain_id2ijyA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
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8. Citations (1)

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9. Files and Curves (10)