SAXSdb — 1b48

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

PROTEIN (GLUTATHIONE S-TRANSFERASE)

Mus musculus

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 2–222 Chain B； UniProt 2–222	Not recorded	HAG 4-S-GLUTATHIONYL-5-PENTYL-TETRAHYDRO-FURAN-2-OL × 1 GSH Glutathione × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；CRYSTALS WERE GROWN IN HANGING DROPS WHICH INITIALLY CONSISTED OF 0.11 MM PROTEIN IN 0.047 M HEPES BUFFER (PH 7.5) CONTAINING 1.82 MM GLUTATHIONE, 10.91 MM HNA-SG (GSH CONJUGATE OF 4-HYDROXYNONENAL), 9.1% ETHANOL, 4.5% ISOPROPANOL, AND 6.5% PEG MONOMETHYL ETHER 5K (PH 7.5). THE DROPS WERE EQUILIBRATED AT 293 K AGAINST WELL SOLUTION CONTAINING 10% ISOPROPANOL AND 12% PEG MONOMETHYL ETHER 5K IN 80 MM HEPES BUFFER (PH 7.5).	Resolution 2.60 Å R-free 0.317

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 1B48	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GUK CRYSTAL STRUCTURE OF MURINE ALPHA-CLASS GSTA4-4 Deposited 1997-12-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–222（222 aa） Chain B 1–222（222 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；CRYSTALLIZATION BY HANGING DROP VAPOR DIFFUSION RESERVOIR: 9% PEG 8000, 0.1 M TRIS/HCL PH 8.1, 5% MPD PROTEIN: 10 MG/ML DISSOLVED IN H20 DROP: 5 + 5 MICROLITER, vapor diffusion - hanging drop	Resolution 2.90 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GSTA4_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–221； UniProt 2–222 Author chain B； PDBConstruct 1–221； UniProt 2–222

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	1b48
Deposition date deposition_date	1999-01-06
Structure title title	CRYSTAL STRUCTURE OF MGSTA4-4 IN COMPLEX WITH GSH CONJUGATE OF 4-HYDROXYNONENAL IN ONE SUBUNIT AND GSH IN THE OTHER: EVIDENCE OF SIGNALING ACROSS DIMER INTERFACE IN MGSTA4-4
Keywords keywords	GLUTATHIONE S-TRANSFERASE, GST, SUBUNIT COOPERATIVITY, TRANSFERASE; TRANSFERASE
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	22.86 Å
Radius of gyration Rg (electron density) rg_electron	21.73 Å
Forward intensity I(0) i0	39565100.00
Molecular weight molecular_weight	51660.0 kDa
Excluded volume excluded_volume	65936 Å³
Envelope volume envelope_volume	76795 Å³
Hydration-shell volume shell_volume	28325 Å³
Envelope diameter envelope_diameter	67.1 Å
Shell Rg shell_rg	29.45 Å
Envelope Rg envelope_rg	21.69 Å
Shape Rg shape_rg	21.74 Å
Total Rg total_rg	22.63 Å
Total atoms total_atoms	3637
Residues n_residues	442
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	66.3 Å
Rg (real space) rg_real	22.67 Å
Rg uncertainty (real space) rg_real_error	0.22 Å
I(0) (real space) i0_real	3.9570e+07
I(0) uncertainty (real space) i0_real_error	4.3570e+05
Rg (reciprocal space) rg_reciprocal	22.72 Å
I(0) (reciprocal space) i0_reciprocal	39570000.0000
Solution quality estimate total_estimate	0.9089
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.6 Å
Skewness Skewness skewness	0.054
Kurtosis Kurtosis kurtosis	-0.541
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10760000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.962

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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	PROTEIN (GLUTATHIONE S-TRANSFERASE)
Molecular weight formula_weight	25476.7 kDa
EC 编号 ec_number	2.5.1.18
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	3677

AAKPKLYYFNGRGRMESIRWLLAAAGVEFEEEFLETREQYEKMQKDGHLLFGQVPLVEIDGMMLTQTRAILSYLAAKYNLYGKDLKERVRIDMYADGTQDLMMMIAVAPFKTPKEKEESYDLILSRAKTRYFPVFEKILKDHGEAFLVGNQLSWADIQLLEAILMVEELSAPVLSDFPLLQAFKTRISNIPTIKKFLQPGSQRKPPPDGPYVEVVRIVLKF

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 2 Entity 2 non-polymer

Description description	4-S-GLUTATHIONYL-5-PENTYL-TETRAHYDRO-FURAN-2-OL
Molecular weight formula_weight	463.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GLUTATHIONE
Molecular weight formula_weight	307.3 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	40

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1b48a1
Class class	a — All alpha proteins
Fold Fold fold	a.45 — GST C-terminal domain-like
Superfamily Superfamily superfamily	a.45.1 — GST C-terminal domain-like
Family Family family	a.45.1.1 — Glutathione S-transferase (GST), C-terminal domain

Domain ID domain_id	d1b48a2
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.47.1.5 — Glutathione S-transferase (GST), N-terminal domain

Domain ID domain_id	d1b48b1
Class class	a — All alpha proteins
Fold Fold fold	a.45 — GST C-terminal domain-like
Superfamily Superfamily superfamily	a.45.1 — GST C-terminal domain-like
Family Family family	a.45.1.1 — Glutathione S-transferase (GST), C-terminal domain

Domain ID domain_id	d1b48b2
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.47.1.5 — Glutathione S-transferase (GST), N-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id	1b48A01
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	1b48A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1b48B01
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	1b48B02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

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8. Citations (2)

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Unit-cell length a length_a	114.450 Å
Unit-cell length b length_b	96.140 Å
Unit-cell length c length_c	50.840 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2440
R_work r_work	0.2440
R_free r_free	0.3170

fit	/app/data/saxs_computation/b4/1b48/1b48.fit
pddf	/app/data/pr_computation/b4/1b48/1b48.pr.out
profile	/app/data/saxs_computation/b4/1b48/1b48.dat

CRYSTAL STRUCTURE OF MGSTA4-4 IN COMPLEX WITH GSH CONJUGATE OF 4-HYDROXYNONENAL IN ONE SUBUNIT AND GSH IN THE OTHER: EVIDENCE OF SIGNALING ACROSS DIMER INTERFACE IN MGSTA4-4

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

PROTEIN (GLUTATHIONE S-TRANSFERASE)

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