SAXSdb — 1b4p

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

PROTEIN (GLUTATHIONE S-TRANSFERASE)

Rattus norvegicus

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 2–218	Fragment：COMPLETE PROTEIN	SO4 SULFATE ION × 6 GPS L-gamma-glutamyl-S-[(9S,10S)-10-hydroxy-9,10-dihydrophenanthren-9-yl]-L-cysteinylglycine × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；PROTEIN CONC. 10 MG/ML, 25 MM TRIS BUFFER (PH 8.0), 1 MM EDTA, 0.3% OCTYL BETA- D-GLUCOPYRANOSIDE, 2 MM PRODUCT INHIBITOR (GPS)	Resolution 1.70 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	GSTM2_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–217； UniProt 2–218

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	1b4p
Deposition date deposition_date	1998-12-26
Structure title title	CRYSTAL STRUCTURES OF CLASS MU CHIMERIC GST ISOENZYMES M1-2 AND M2-1
Keywords keywords	CHIMERIC GST, 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	18.77 Å
Radius of gyration Rg (electron density) rg_electron	17.59 Å
Forward intensity I(0) i0	12506700.00
Molecular weight molecular_weight	26997.0 kDa
Excluded volume excluded_volume	33947 Å³
Envelope volume envelope_volume	38120 Å³
Hydration-shell volume shell_volume	18032 Å³
Envelope diameter envelope_diameter	59.5 Å
Shell Rg shell_rg	23.92 Å
Envelope Rg envelope_rg	17.89 Å
Shape Rg shape_rg	17.58 Å
Total Rg total_rg	18.59 Å
Total atoms total_atoms	1898
Residues n_residues	217
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	59.1 Å
Rg (real space) rg_real	18.66 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	1.2510e+07
I(0) uncertainty (real space) i0_real_error	1.3410e+05
Rg (reciprocal space) rg_reciprocal	18.68 Å
I(0) (reciprocal space) i0_reciprocal	12510000.0000
Solution quality estimate total_estimate	0.8943
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.3 Å
Skewness Skewness skewness	0.162
Kurtosis Kurtosis kurtosis	-0.423
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3139000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.961

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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	25740.7 kDa
EC 编号 ec_number	2.5.1.18
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	2148

PMILGYWNVRGLTHPIRLLLEYTDSSYEEKRYAMGDAPDYDRSQWLNEKFKLGLDFPNLPYLIDGSRKITQSNAIMRYLARKHHLCGETEEERIRVDVLENQAMDTRLQLAMVCYSPDFERKKPEYLEGLPEKMKLYSEFLGKQPWFAGNKITYVDFLVYDVLDQHRIFEPKCLDAFPNLKDFVARFEGLKKISDYMKSGRFLSKPIFAKMAFWNPK

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	L-gamma-glutamyl-S-[(9S,10S)-10-hydroxy-9,10-dihydrophenanthren-9-yl]-L-cysteinylglycine
Molecular weight formula_weight	501.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	250

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1b4pa1
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	d1b4pa2
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 (2 domains)

Domain ID domain_id	1b4pA01
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	1b4pA02
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 (4)

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Unit-cell length a length_a	73.590 Å
Unit-cell length b length_b	82.550 Å
Unit-cell length c length_c	79.570 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	1.700 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1790
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/b4/1b4p/1b4p.fit
pddf	/app/data/pr_computation/b4/1b4p/1b4p.pr.out
profile	/app/data/saxs_computation/b4/1b4p/1b4p.dat

CRYSTAL STRUCTURES OF CLASS MU CHIMERIC GST ISOENZYMES M1-2 AND M2-1

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