Cryo-EM structure of GroEL-gammaATP

Method: ELECTRON MICROSCOPY D_max: 171.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ykc
deposition_date	2025-10-06
title	Cryo-EM structure of GroEL-gammaATP
keywords	Chaperonin, Tetradecamer, Nucleotide-binding, Allosteric-change, CHAPERONE; CHAPERONE
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	64.42 Å
rg_electron	63.34 Å
i0	8746110000.00
molecular_weight	780030.0 kDa
excluded_volume	974180 Å³
envelope_volume	1576700 Å³
shell_volume	196790 Å³
envelope_diameter	186.6 Å
shell_rg	75.32 Å
envelope_rg	59.65 Å
shape_rg	63.38 Å
total_rg	63.42 Å
total_atoms	54473
n_residues	7350
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	171.7 Å
rg_real	63.69 Å
rg_real_error	0.74 Å
i0_real	8.7460e+09
i0_real_error	1.7070e+08
rg_reciprocal	65.03 Å
i0_reciprocal	8766000000.0000
total_estimate	0.8371
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	93.0 Å
skewness	-0.103
kurtosis	-0.537
angular_range	— – 0.1200 Å⁻¹
current_alpha	0.0000
highest_alpha	4392000000.0000
n_real_points	25
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.001

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (2)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.300 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.30 Å
resolution_method	—
num_particles	261106

description	Chaperonin GroEL
formula_weight	55349.3 kDa
ec_number	5.6.1.7
src_method	man
entity_count	14

Cryo-EM structure of GroEL-gammaATP

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N
atom_count	54473

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
formula_weight	523.2 kDa
src_method	syn
entity_count	14

fit	/app/data/saxs_computation/yk/9ykc/9ykc.fit
pddf	/app/data/pr_computation/yk/9ykc/9ykc.pr.out
profile	/app/data/saxs_computation/yk/9ykc/9ykc.dat