SAXSdb — 1u3a

▼

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

Thiol: disulfide interchange protein dsbA

Escherichia coli

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 20–208 Chain B； UniProt 20–208 Chain D； UniProt 20–208 Chain E； UniProt 20–208	Mutation：C33A	PE5 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；281 K；PEG-MME550, Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K, pH 6.50	Resolution 2.00 Å R-free 0.272

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 1U3A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A23 SOLUTION NMR STRUCTURE OF REDUCED DSBA FROM ESCHERICHIA COLI, MINIMIZED AVERAGE STRUCTURE Deposited 1998-01-15	Different construct Different mutation/modification Different oligomeric state 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 20–208（189 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3.7；300 K；Ionic strength (raw mmCIF value) 20mM；Pressure 1013 NMR sample composition 20 MM SODIUM PHOSPHATE IN H2O	Resolution not provided
1A24 SOLUTION NMR STRUCTURE OF REDUCED DSBA FROM ESCHERICHIA COLI, FAMILY OF 20 STRUCTURES Deposited 1998-01-15	Different construct Different mutation/modification Different oligomeric state 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 20–208（189 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3.7；300 K；Ionic strength (raw mmCIF value) 20mM；Pressure 1013 NMR sample composition 20 MM SODIUM PHOSPHATE IN H2O	Resolution not provided
1A2J OXIDIZED DSBA CRYSTAL FORM II Deposited 1998-01-06	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 20–208（189 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；27% PEG 4K IN 0.1M ACETATE BUFFER PH 5.0	Resolution 2.00 Å R-free 0.227
1A2L REDUCED DSBA AT 2.7 ANGSTROMS RESOLUTION Deposited 1998-01-06	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 20–208（189 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；0.2 M AMMONIUM ACETATE, 0.1M SODIUM CITRATE PH 5.6 30% (W/V) PEG 4000 AND 40MM DTT.	Resolution 2.70 Å R-free 0.285
1A2L REDUCED DSBA AT 2.7 ANGSTROMS RESOLUTION Deposited 1998-01-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 20–208（189 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；0.2 M AMMONIUM ACETATE, 0.1M SODIUM CITRATE PH 5.6 30% (W/V) PEG 4000 AND 40MM DTT.	Resolution 2.70 Å R-free 0.285
1A2M OXIDIZED DSBA AT 2.7 ANGSTROMS RESOLUTION, CRYSTAL FORM III Deposited 1998-01-06	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 20–208（189 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；0.2 M AMMONIUM ACETATE, 0.1M SODIUM CITRATE PH 5.6 30% (W/V) PEG 4000.	Resolution 2.70 Å R-free 0.308
1A2M OXIDIZED DSBA AT 2.7 ANGSTROMS RESOLUTION, CRYSTAL FORM III Deposited 1998-01-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 20–208（189 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；0.2 M AMMONIUM ACETATE, 0.1M SODIUM CITRATE PH 5.6 30% (W/V) PEG 4000.	Resolution 2.70 Å R-free 0.308
1AC1 DSBA MUTANT H32L Deposited 1997-02-10	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 20–208（189 aa） Chain B 20–208（189 aa）	Mutation：H32L Mutation：H32L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.3；CACODYLATE PH 6.3 PEG 8K 25%	Resolution 2.00 Å R-free 0.220
1ACV DSBA MUTANT H32S Deposited 1997-02-10	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 20–208（189 aa） Chain B 20–208（189 aa）	Mutation：H32S Mutation：H32S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.3；CACODYLATE PH 6.3, PEG 8K 25%	Resolution 1.90 Å R-free 0.216
1BQ7 DSBA MUTANT P151A, ROLE OF THE CIS-PROLINE IN THE ACTIVE SITE OF DSBA Deposited 1998-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 20–208（189 aa） Chain B 20–208（189 aa） Chain C 20–208（189 aa） Chain D 20–208（189 aa） Chain E 20–208（189 aa） Chain F 20–208（189 aa）	Mutation：P151A Mutation：P151A Mutation：P151A Mutation：P151A Mutation：P151A Mutation：P151A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；25% PEG 8,000 100 MM NACL 100 MM SODIUM CACODYLATE, PH 6.5 10% DMSO DIFFUSION VAPOR AT ROOM TEMPERATURE, SEEDING	Resolution 2.80 Å R-free 0.289
1DSB CRYSTAL STRUCTURE OF THE DSBA PROTEIN REQUIRED FOR DISULPHIDE BOND FORMATION IN VIVO Deposited 1993-05-24	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 20–208（189 aa） Chain B 20–208（189 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1FVJ THE 2.06 ANGSTROM STRUCTURE OF THE H32Y MUTANT OF THE DISULFIDE BOND FORMATION PROTEIN (DSBA) Deposited 1996-08-28	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 20–208（189 aa）	Mutation：H32Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.06 Å R-free 0.218
1FVJ THE 2.06 ANGSTROM STRUCTURE OF THE H32Y MUTANT OF THE DISULFIDE BOND FORMATION PROTEIN (DSBA) Deposited 1996-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 20–208（189 aa）	Mutation：H32Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.06 Å R-free 0.218
1FVK THE 1.7 ANGSTROM STRUCTURE OF WILD TYPE DISULFIDE BOND FORMATION PROTEIN (DSBA) Deposited 1996-08-28	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 20–208（189 aa） Chain B 20–208（189 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.70 Å R-free 0.231
1TI1 crystal structure of a mutant DsbA Deposited 2004-06-02	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 20–208（189 aa）	Mutation：C33A	D12 DODECANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；281 K；PEG 8000, Bicine, DDM, MPD, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K	Resolution 2.60 Å R-free 0.279
1UN2 Crystal structure of circularly permuted CPDSBA_Q100T99: Preserved Global Fold and Local Structural Adjustments Deposited 2003-09-03	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 119–208（90 aa） Fragment：THIOREDOXIN-LIKE DOMAIN, HELICAL DOMAIN RESIDUES, 119-208 Chain A 20–118（99 aa） Fragment：THIOREDOXIN-LIKE DOMAIN, HELICAL DOMAIN RESIDUES, 119-208	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；25% PEG 8000, 7-10% DMSO, 0.1M NA CACODYLATE PH 6.5	Resolution 2.40 Å R-free 0.256

13 other PDB entries and 16 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 Author chain B； PDBConstruct 1–189； UniProt 20–208 Author chain D； PDBConstruct 1–189； UniProt 20–208 Author chain E； PDBConstruct 1–189； UniProt 20–208

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1u3a
Deposition date deposition_date	2004-07-21
Structure title title	mutant DsbA
Keywords keywords	thiol oxidoreductase, thiol disulfide interchange, thioredoxin, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	32.70 Å
Radius of gyration Rg (electron density) rg_electron	32.31 Å
Forward intensity I(0) i0	106112000.00
Molecular weight molecular_weight	83530.0 kDa
Excluded volume excluded_volume	105150 Å³
Envelope volume envelope_volume	134790 Å³
Hydration-shell volume shell_volume	35751 Å³
Envelope diameter envelope_diameter	110.5 Å
Shell Rg shell_rg	37.99 Å
Envelope Rg envelope_rg	31.99 Å
Shape Rg shape_rg	32.30 Å
Total Rg total_rg	32.83 Å
Total atoms total_atoms	5889
Residues n_residues	749
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

▼

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

Maximum dimension Dmax dmax	107.2 Å
Rg (real space) rg_real	32.79 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	1.0610e+08
I(0) uncertainty (real space) i0_real_error	1.6340e+06
Rg (reciprocal space) rg_reciprocal	32.76 Å
I(0) (reciprocal space) i0_reciprocal	106100000.0000
Solution quality estimate total_estimate	0.8885
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	35.7 Å
Skewness Skewness skewness	0.362
Kurtosis Kurtosis kurtosis	-0.512
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15700000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.907

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Thiol: disulfide interchange protein dsbA
Molecular weight formula_weight	21123.0 kDa
Mutation mutation	C33A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,E
Atom count atom_count	6148

AQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHAYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEKK

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
Molecular weight formula_weight	398.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	259

▼

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1u3aa_
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	d1u3ab_
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	d1u3ad_
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	d1u3ae_
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 (4 domains)

Domain ID domain_id	1u3aA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	1u3aB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	1u3aD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	1u3aE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

▶

8. Citations (1)

▶

Unit-cell length a length_a	46.956 Å
Unit-cell length b length_b	82.282 Å
Unit-cell length c length_c	113.910 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.74 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	45.000 Å
R factor r_factor	0.2160
R_work r_work	0.2090
R_free r_free	0.2720

fit	/app/data/saxs_computation/u3/1u3a/1u3a.fit
pddf	/app/data/pr_computation/u3/1u3a/1u3a.pr.out
profile	/app/data/saxs_computation/u3/1u3a/1u3a.dat

mutant DsbA

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