SAXSdb — 1bed

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

DSBA OXIDOREDUCTASE

OrganismNot specified

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 20–200	Not recorded	No other associated polymer	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

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 1BED	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2IJY NMR structure ensemble for the reduced DsbA disulphide oxidoreductase from Vibrio Cholerae Deposited 2006-10-02	Different oligomeric state 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	No recorded non-water small molecule	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
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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bed
Deposition date deposition_date	1996-09-16
Structure title title	STRUCTURE OF DISULFIDE OXIDOREDUCTASE
Keywords keywords	TCPG, PROTEIN DISULFIDE ISOMERASE, DISULFIDE OXIDOREDUCTASE, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	17.87 Å
Radius of gyration Rg (electron density) rg_electron	16.74 Å
Forward intensity I(0) i0	7099300.00
Molecular weight molecular_weight	19492.0 kDa
Excluded volume excluded_volume	24338 Å³
Envelope volume envelope_volume	28213 Å³
Hydration-shell volume shell_volume	14586 Å³
Envelope diameter envelope_diameter	58.5 Å
Shell Rg shell_rg	22.14 Å
Envelope Rg envelope_rg	16.95 Å
Shape Rg shape_rg	16.75 Å
Total Rg total_rg	17.65 Å
Total atoms total_atoms	1374
Residues n_residues	181
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	59.4 Å
Rg (real space) rg_real	17.85 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	7.0990e+06
I(0) uncertainty (real space) i0_real_error	8.4150e+04
Rg (reciprocal space) rg_reciprocal	17.85 Å
I(0) (reciprocal space) i0_reciprocal	7099000.0000
Solution quality estimate total_estimate	0.8759
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.7 Å
Skewness Skewness skewness	0.332
Kurtosis Kurtosis kurtosis	-0.312
Angular range angular_range	— – 0.4450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1866000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.796; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 1.000

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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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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1beda_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.13 — DsbA-like

CATH v4.4 (1 domains)

Domain ID domain_id	1bedA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

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8. Citations (2)

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Unit-cell length a length_a	64.000 Å
Unit-cell length b length_b	91.500 Å
Unit-cell length c length_c	64.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2050
R_work r_work	0.2050
R_free r_free	0.2410

Description description	DSBA OXIDOREDUCTASE
Molecular weight formula_weight	20523.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1438

STRUCTURE OF DISULFIDE OXIDOREDUCTASE

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

DSBA OXIDOREDUCTASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	53

fit	/app/data/saxs_computation/be/1bed/1bed.fit
pddf	/app/data/pr_computation/be/1bed/1bed.pr.out
profile	/app/data/saxs_computation/be/1bed/1bed.dat