SAXSdb — 1paq

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

Translation initiation factor eIF-2B epsilon subunit

Saccharomyces cerevisiae

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 524–712	Fragment：catalytic domain, residues (524-712) Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.75；277 K；PEG 2000MME, ammonium acetate, Tris-HCl, pH 5.75, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.30 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 1PAQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6I3M eIF2B:eIF2 complex, phosphorylated on eIF2 alpha serine 52. Deposited 2018-11-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain G 1–712（712 aa） Chain H 1–712（712 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Solutions for sample preparation were made fresh, filter sterilized, and degassed. cryo-EM vitrification conditions Cryogen ETHANE；Blot for 2 seconds before plunging	Resolution 3.93 Å
6I7T eIF2B:eIF2 complex Deposited 2018-11-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain G 1–712（712 aa） Chain H 1–712（712 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Solutions for sample preparation were made fresh, filter sterilized, and degassed. cryo-EM vitrification conditions Cryogen ETHANE；Blot for 1 second before plunging	Resolution 4.61 Å
6QG0 Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model 1) Deposited 2019-01-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain I 1–712（712 aa） Chain J 1–712（712 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.15 Å
6QG1 Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model 2) Deposited 2019-01-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain I 1–712（712 aa） Chain J 1–712（712 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.25 Å
6QG2 Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model A) Deposited 2019-01-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain I 1–712（712 aa） Chain J 1–712（712 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.55 Å
6QG3 Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model B) Deposited 2019-01-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain I 1–712（712 aa） Chain J 1–712（712 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.40 Å
6QG5 Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model C) Deposited 2019-01-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain I 1–712（712 aa） Chain J 1–712（712 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 10.10 Å
6QG6 Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model D) Deposited 2019-01-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain I 1–712（712 aa） Chain J 1–712（712 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 10.40 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EI2BE_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–189； UniProt 524–712

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	1paq
Deposition date deposition_date	2003-05-14
Structure title title	CRYSTAL STRUCTURE OF THE CATALYTIC FRAGMENT OF EUKARYOTIC INITIATION FACTOR 2B EPSILON
Keywords keywords	heat repeat, aa motif, TRANSLATION; TRANSLATION
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	16.89 Å
Radius of gyration Rg (electron density) rg_electron	15.40 Å
Forward intensity I(0) i0	6818180.00
Molecular weight molecular_weight	19230.0 kDa
Excluded volume excluded_volume	24055 Å³
Envelope volume envelope_volume	26397 Å³
Hydration-shell volume shell_volume	14475 Å³
Envelope diameter envelope_diameter	51.2 Å
Shell Rg shell_rg	21.36 Å
Envelope Rg envelope_rg	15.69 Å
Shape Rg shape_rg	15.39 Å
Total Rg total_rg	16.52 Å
Total atoms total_atoms	1341
Residues n_residues	156
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	53.2 Å
Rg (real space) rg_real	16.79 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	6.8180e+06
I(0) uncertainty (real space) i0_real_error	7.2900e+04
Rg (reciprocal space) rg_reciprocal	16.80 Å
I(0) (reciprocal space) i0_reciprocal	6818000.0000
Solution quality estimate total_estimate	0.8955
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	51.1 Å
Skewness Skewness skewness	0.131
Kurtosis Kurtosis kurtosis	-0.439
Angular range angular_range	— – 0.4700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1160000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.962

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1paqa_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.14 — MIF4G domain-like

CATH v4.4 (1 domains)

Domain ID domain_id	1paqA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	180 —

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8. Citations (1)

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Unit-cell length a length_a	106.340 Å
Unit-cell length b length_b	106.340 Å
Unit-cell length c length_c	91.710 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	16

Space group space_group	I 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2439
R_work r_work	0.2426
R_free r_free	0.2723

Description description	Translation initiation factor eIF-2B epsilon subunit
Molecular weight formula_weight	22573.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1431

CRYSTAL STRUCTURE OF THE CATALYTIC FRAGMENT OF EUKARYOTIC INITIATION FACTOR 2B EPSILON

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

Translation initiation factor eIF-2B epsilon subunit

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	90

fit	/app/data/saxs_computation/pa/1paq/1paq.fit
pddf	/app/data/pr_computation/pa/1paq/1paq.pr.out
profile	/app/data/saxs_computation/pa/1paq/1paq.dat