2leg

Membrane protein complex DsbB-DsbA structure by joint calculations with solid-state NMR and X-ray experimental data

Method: SOLID-STATE NMR Dmax: 81.4 Å Quality: GOOD

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

Thiol:disulfide interchange protein DsbA

Escherichia coli

UniProt P0AEG4

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 20–208 Mutation:C33A Disulfide bond formation protein B × 1 (P0A6M2) ZN ZINC ION × 1 UQ1 UBIQUINONE-1 × 1 SOLID-STATE NMR NMR measurement conditions:pH 7;270 K;Pressure ambient NMR measurement conditions:pH 7.8;261 K;Pressure ambient NMR sample composition:15 mg [U-100% 13C; U-100% 15N] DsbA, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:10 mg [2-13C-glycerol; U-15N] DsbA, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:10 mg [1,3-13C-glycerol; U-15N] DsbA, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:7 mg [U-100% 13C; U-100% 15N] DsbB, 2 mg DDM, 7 mg E. coli lipids, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:5 mg [2-13C-glycerol; U-15N] DsbB, 2 mg DDM, 7 mg E. coli lipids, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:4 mg [1,3-13C-glycerol; U-15N] DsbB, 2 mg DDM, 7 mg E. coli lipids, 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.

75 other PDB entries and 152 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DSBA_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–189; UniProt 20–208

Disulfide bond formation protein B

Escherichia coli

UniProt P0A6M2

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1–176 Mutation:C8A, C49V, C130S Thiol:disulfide interchange protein DsbA × 1 (P0AEG4) ZN ZINC ION × 1 UQ1 UBIQUINONE-1 × 1 SOLID-STATE NMR NMR measurement conditions:pH 7;270 K;Pressure ambient NMR measurement conditions:pH 7.8;261 K;Pressure ambient NMR sample composition:15 mg [U-100% 13C; U-100% 15N] DsbA, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:10 mg [2-13C-glycerol; U-15N] DsbA, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:10 mg [1,3-13C-glycerol; U-15N] DsbA, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:7 mg [U-100% 13C; U-100% 15N] DsbB, 2 mg DDM, 7 mg E. coli lipids, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:5 mg [2-13C-glycerol; U-15N] DsbB, 2 mg DDM, 7 mg E. coli lipids, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:4 mg [1,3-13C-glycerol; U-15N] DsbB, 2 mg DDM, 7 mg E. coli lipids, 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.

8 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DSBB_ECOLI
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–176; UniProt 1–176

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 2leg

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2leg
Deposition date deposition_date2011-06-15
Structure title titleMembrane protein complex DsbB-DsbA structure by joint calculations with solid-state NMR and X-ray experimental data
Keywords keywords;Disulfide bond, membrane protein, redox-active center, cell inner membrane, cell membrane, chaperone, electron transport, membrane, oxidoreductase, transmembrane, transport ;; MEMBRANE PROTEIN, OXIDOREDUCTASE
Experimental Method methodSOLID-STATE NMR

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

Radius of gyration Rg (Guinier) rg_guinier22.61
Radius of gyration Rg (electron density) rg_electron23.22
Forward intensity I(0) i01557170000.00
Molecular weight molecular_weight365280.0 kDa
Excluded volume excluded_volume468690 ų
Envelope volume envelope_volume76923 ų
Hydration-shell volume shell_volume26931 ų
Envelope diameter envelope_diameter90.1
Shell Rg shell_rg30.82
Envelope Rg envelope_rg24.50
Shape Rg shape_rg23.20
Total Rg total_rg23.44
Total atoms total_atoms51540
Residues n_residues3220
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 dmax81.4
Rg (real space) rg_real22.68
Rg uncertainty (real space) rg_real_error0.85
I(0) (real space) i0_real1.5570e+09
I(0) uncertainty (real space) i0_real_error2.5550e+07
Rg (reciprocal space) rg_reciprocal22.67
I(0) (reciprocal space) i0_reciprocal1557000000.0000
Solution quality estimate total_estimate0.8517
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.4
Skewness Skewness skewness0.454
Kurtosis Kurtosis kurtosis-0.132
Angular range angular_range— – 0.3500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2668000.0000
Real-space data points n_real_points67
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: 0.888; Smooth: 0.992

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id2legA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id2legB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1550 — Bromodomain-like
Homologous superfamily homologous superfamily10 — DsbB-like

8. Citations (1)

9. Files and Curves (10)