SAXSdb — 1oaz

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

THIOREDOXIN 1

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–34 Chain A； UniProt 35–108	Fragment：TRX-SHEAR3, RESIDUES 1-123	IMMUNOGLOBULIN E × 1 IMMUNOGLOBULIN E × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5；21% PEG 8K, 0.1M NA CACODYLATE, 0.2M NA ACETATE PH5.5, pH 5.00	Resolution 2.78 Å R-free 0.276
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 1–34 Chain B； UniProt 35–108	Fragment：TRX-SHEAR3, RESIDUES 1-123	IMMUNOGLOBULIN E × 1 IMMUNOGLOBULIN E × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5；21% PEG 8K, 0.1M NA CACODYLATE, 0.2M NA ACETATE PH5.5, pH 5.00	Resolution 2.78 Å R-free 0.276

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 1OAZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1M7T Solution Structure and Dynamics of the Human-Escherichia coli Thioredoxin Chimera: Insights into Thermodynamic Stability Deposited 2002-07-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 68–107（40 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；308 K NMR sample composition 1 mM protein in 100 mM sodium phosphate buffer (pH 7.0), 20 M EDTA, 0.02% sodium azide, and 10% D2O. \| 90% H2O/10% D2O	Resolution not provided
1ZZY Crystal Structure of Thioredoxin Mutant L7V Deposited 2005-06-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–108（108 aa）	Mutation：L7V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions COUNTER-DIFFUSION；pH 3.8；295 K；10 mM AcNa pH 3.8, 25% (v/v) EtOH, 10 mM Ac2Cu, Counter-diffusion, temperature 295K	Resolution 2.50 Å R-free 0.274
1ZZY Crystal Structure of Thioredoxin Mutant L7V Deposited 2005-06-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–108（108 aa）	Mutation：L7V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions COUNTER-DIFFUSION；pH 3.8；295 K；10 mM AcNa pH 3.8, 25% (v/v) EtOH, 10 mM Ac2Cu, Counter-diffusion, temperature 295K	Resolution 2.50 Å R-free 0.274
2BTO Structure of BtubA from Prosthecobacter dejongeii Deposited 2005-06-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain T 1–108（108 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions 1.6M NA K PHOSPHATE, PH 6.0	Resolution 2.50 Å R-free 0.235

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	THIO_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–35； UniProt 1–34 Author chain A； PDBConstruct 50–123； UniProt 35–108 Author chain B； PDBConstruct 2–35； UniProt 1–34 Author chain B； PDBConstruct 50–123； UniProt 35–108

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	1oaz
Deposition date deposition_date	2003-01-21
Structure title title	IgE Fv SPE7 complexed with a recombinant thioredoxin
Keywords keywords	;IMMUNE SYSTEM, ANTIBODY-COMPLEX, ANTIBODY, ALLERGY, IGE, CONFORMATIONAL DIVERSITY, MULTISPECFICITY, REDOX-ACTIVE CENTER, ELECTRON TRANSPORT ;; IMMUNE SYSTEM
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	38.96 Å
Radius of gyration Rg (electron density) rg_electron	38.82 Å
Forward intensity I(0) i0	84212800.00
Molecular weight molecular_weight	74857.0 kDa
Excluded volume excluded_volume	93920 Å³
Envelope volume envelope_volume	131400 Å³
Hydration-shell volume shell_volume	29319 Å³
Envelope diameter envelope_diameter	128.2 Å
Shell Rg shell_rg	42.74 Å
Envelope Rg envelope_rg	37.51 Å
Shape Rg shape_rg	38.81 Å
Total Rg total_rg	39.13 Å
Total atoms total_atoms	5278
Residues n_residues	690
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	127.5 Å
Rg (real space) rg_real	39.30 Å
Rg uncertainty (real space) rg_real_error	1.34 Å
I(0) (real space) i0_real	8.4210e+07
I(0) uncertainty (real space) i0_real_error	1.6760e+06
Rg (reciprocal space) rg_reciprocal	39.10 Å
I(0) (reciprocal space) i0_reciprocal	84200000.0000
Solution quality estimate total_estimate	0.7765
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.9 Å
Skewness Skewness skewness	0.280
Kurtosis Kurtosis kurtosis	-0.981
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10370000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.563; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.517; Smooth: 0.884

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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	THIOREDOXIN 1
Molecular weight formula_weight	13466.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5639

MSDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPIEESDDRRYDLVGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLA

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 polymer

Description description	IMMUNOGLOBULIN E
Molecular weight formula_weight	13687.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,J

EVQLQQSGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNGGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARMWYYGTYYFDYWGQGTTLTVSSAA

来源 Source

来源生物 organism	MUS MUSCULUS
通用名 common_name	HOUSE MOUSE
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 polymer

Description description	IMMUNOGLOBULIN E
Molecular weight formula_weight	11530.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,N

QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHLVFGGGTKLTVLT

来源 Source

来源生物 organism	MUS MUSCULUS
通用名 common_name	HOUSE MOUSE
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	ESCHERICHIA COLI

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	361

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1oaza_
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.47.1.1 — Thioltransferase

Domain ID domain_id	d1oazb_
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.47.1.1 — Thioltransferase

Domain ID domain_id	d1oazh_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1oazj_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1oazl_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1oazn_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (6 domains)

Domain ID domain_id	1oazA00
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	1oazB00
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	1oazH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1oazJ00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1oazL00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1oazN00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	79.352 Å
Unit-cell length b length_b	79.467 Å
Unit-cell length c length_c	170.763 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.780 Å
Low-resolution limit resolution_low	30.150 Å
R factor r_factor	—
R_work r_work	0.2080
R_free r_free	0.2760

fit	/app/data/saxs_computation/oa/1oaz/1oaz.fit
pddf	/app/data/pr_computation/oa/1oaz/1oaz.pr.out
profile	/app/data/saxs_computation/oa/1oaz/1oaz.dat

IgE Fv SPE7 complexed with a recombinant thioredoxin

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

THIOREDOXIN 1

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)