1bye

GLUTATHIONE S-TRANSFERASE I FROM MAIS IN COMPLEX WITH ATRAZINE GLUTATHIONE CONJUGATE

Method: X-RAY DIFFRACTION D_max: 118.9 Å Quality: GOOD

▼

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

PROTEIN (GLUTATHIONE S-TRANSFERASE)

Zea mays

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 1–213 Chain B； UniProt 1–213	Not recorded	ATA ATRAZINE GLUTATHIONE CONJUGATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.00	Resolution 2.80 Å R-free 0.305
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–213 Chain D； UniProt 1–213	Not recorded	ATA ATRAZINE GLUTATHIONE CONJUGATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.00	Resolution 2.80 Å R-free 0.305
3	Protein homooligomer Homooligomer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 1–213 Chain B； UniProt 1–213 Chain C； UniProt 1–213 Chain D； UniProt 1–213	Not recorded	ATA ATRAZINE GLUTATHIONE CONJUGATE × 8	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.00	Resolution 2.80 Å R-free 0.305
4	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–213 Chain B； UniProt 1–213 Chain C； UniProt 1–213 Chain D； UniProt 1–213	Not recorded	ATA ATRAZINE GLUTATHIONE CONJUGATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.00	Resolution 2.80 Å R-free 0.305

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 1BYE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AXD STRUCTURE OF GLUTATHIONE S-TRANSFERASE-I BOUND WITH THE LIGAND LACTOYLGLUTATHIONE Deposited 1997-10-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–209（209 aa） Chain B 1–209（209 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.50 Å

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

View Construct and Data Evidence

UniProt name	GSTF1_MAIZE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–213； UniProt 1–213 Author chain B； PDBConstruct 1–213； UniProt 1–213 Author chain C； PDBConstruct 1–213； UniProt 1–213 Author chain D； PDBConstruct 1–213； UniProt 1–213

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bye
Deposition date deposition_date	1998-10-14
Structure title title	GLUTATHIONE S-TRANSFERASE I FROM MAIS IN COMPLEX WITH ATRAZINE GLUTATHIONE CONJUGATE
Keywords keywords	GLUTATHIONE S-TRANSFERASE, HERBICIDE, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	36.29 Å
Radius of gyration Rg (electron density) rg_electron	36.30 Å
Forward intensity I(0) i0	135496000.00
Molecular weight molecular_weight	96688.0 kDa
Excluded volume excluded_volume	122090 Å³
Envelope volume envelope_volume	153930 Å³
Hydration-shell volume shell_volume	35694 Å³
Envelope diameter envelope_diameter	127.0 Å
Shell Rg shell_rg	41.75 Å
Envelope Rg envelope_rg	36.08 Å
Shape Rg shape_rg	36.30 Å
Total Rg total_rg	36.69 Å
Total atoms total_atoms	6796
Residues n_residues	852
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	118.9 Å
Rg (real space) rg_real	36.57 Å
Rg uncertainty (real space) rg_real_error	0.96 Å
I(0) (real space) i0_real	1.3550e+08
I(0) uncertainty (real space) i0_real_error	2.3210e+06
Rg (reciprocal space) rg_reciprocal	36.41 Å
I(0) (reciprocal space) i0_reciprocal	135500000.0000
Solution quality estimate total_estimate	0.7924
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.7 Å
Skewness Skewness skewness	0.415
Kurtosis Kurtosis kurtosis	-0.723
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	58090000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.624; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.733; Smooth: 0.692

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PROTEIN (GLUTATHIONE S-TRANSFERASE)
Molecular weight formula_weight	23715.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6844

APMKLYGAVMSWNLTRCATALEEAGSDYEIVPINFATAEHKSPEHLVRNPFGQVPALQDGDLYLFESRAICKYAARKNKPELLREGNLEEAAMVDVWIEVEANQYTAALNPILFQVLISPMLGGTTDQKVVDENLEKLKKVLEVYEARLTKCKYLAGDFLSLADLNHVSVTLCLFATPYASVLDAYPHVKAWWSGLMERPSVQKVAALMKPSA

来源 Source

来源生物 organism	Zea mays
NCBI Class编号 ncbi_taxonomy_id	4577
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ATRAZINE GLUTATHIONE CONJUGATE
Molecular weight formula_weight	486.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	48

▼

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1byea1
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	d1byea2
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	d1byeb1
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	d1byeb2
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	d1byec1
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	d1byec2
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	d1byed1
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	d1byed2
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 (8 domains)

Domain ID domain_id	1byeA01
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	1byeA02
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	1byeB01
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	1byeB02
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	1byeC01
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	1byeC02
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	1byeD01
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	1byeD02
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 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	169.610 Å
Unit-cell length b length_b	60.280 Å
Unit-cell length c length_c	121.430 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	126.22 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.2210
R_free r_free	0.3050

fit	/app/data/saxs_computation/by/1bye/1bye.fit
pddf	/app/data/pr_computation/by/1bye/1bye.pr.out
profile	/app/data/saxs_computation/by/1bye/1bye.dat