SAXSdb — 4dvc

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

Thiol:disulfide interchange protein DsbA

Vibrio cholerae

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 19–200	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

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 4DVC	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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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
2IJY NMR structure ensemble for the reduced DsbA disulphide oxidoreductase from Vibrio Cholerae Deposited 2006-10-02	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 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
7LUI Crystal structure of Vibrio cholerae DsbA in complex with bile salt taurocholate Deposited 2021-02-22	Different construct Different mutation/modification 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 3–184； UniProt 19–200

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	4dvc
Deposition date deposition_date	2012-02-23
Structure title title	Structural and functional studies of TcpG, the Vibrio cholerae DsbA disulfide-forming protein required for pilus and cholera toxin production
Keywords keywords	Cholera, pilus assembly, oxidoreductase, Thioredoxin fold, DsbA-like, Disulfide bond, DsbB; 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	18.67 Å
Radius of gyration Rg (electron density) rg_electron	17.45 Å
Forward intensity I(0) i0	8101080.00
Molecular weight molecular_weight	20958.0 kDa
Excluded volume excluded_volume	26207 Å³
Envelope volume envelope_volume	30656 Å³
Hydration-shell volume shell_volume	15265 Å³
Envelope diameter envelope_diameter	69.8 Å
Shell Rg shell_rg	22.89 Å
Envelope Rg envelope_rg	18.02 Å
Shape Rg shape_rg	17.41 Å
Total Rg total_rg	18.49 Å
Total atoms total_atoms	2908
Residues n_residues	184
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	70.2 Å
Rg (real space) rg_real	18.75 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	8.1010e+06
I(0) uncertainty (real space) i0_real_error	1.0530e+05
Rg (reciprocal space) rg_reciprocal	18.74 Å
I(0) (reciprocal space) i0_reciprocal	8101000.0000
Solution quality estimate total_estimate	0.8004
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	21.2 Å
Skewness Skewness skewness	0.576
Kurtosis Kurtosis kurtosis	0.341
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2053000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.529; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.834; Smooth: 0.979

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Thiol:disulfide interchange protein DsbA
Molecular weight formula_weight	20748.6 kDa
Mutation mutation	R134H, V164A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3281

SNAAQFKEGEHYQVLKTPASSSPVVSEFFSFYCPHCNTFEPIIAQLKQQLPEGAKFQKNHVSFMGGNMGQAMSKAYATMIALEVEDKMVPVMFNRIHTLRKPPKDEQELRQIFLDEGIDAAKFDAAYNGFAVDSMVHRFDKQFQDSGLTGVPAVVVNNRYLVQGQSAKSLDEYFDLVNYLLTLK

来源 Source

来源生物 organism	Vibrio cholerae
NCBI Class编号 ncbi_taxonomy_id	243277
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	284

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4dvca1
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

Domain ID domain_id	d4dvca2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	4dvcA00
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 (1)

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Unit-cell length a length_a	62.654 Å
Unit-cell length b length_b	89.520 Å
Unit-cell length c length_c	64.263 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	1.200 Å
Low-resolution limit resolution_low	32.132 Å
R factor r_factor	0.1198
R_work r_work	0.1191
R_free r_free	0.1392

fit	/app/data/saxs_computation/dv/4dvc/4dvc.fit
pddf	/app/data/pr_computation/dv/4dvc/4dvc.pr.out
profile	/app/data/saxs_computation/dv/4dvc/4dvc.dat

Structural and functional studies of TcpG, the Vibrio cholerae DsbA disulfide-forming protein required for pilus and cholera toxin production

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

Thiol:disulfide interchange protein DsbA

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