SAXSdb — 9wbt

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1. Structure Basics

entry_id	9wbt
deposition_date	2025-08-15
last_revision	2025-09-03
title	Crystal Structure of Escherichia coli GroEL with Magnesium Ions and a Phosphorylated Serine Residue-3.2A
keywords	Escherichia coli GroEL, CHAPERONE; CHAPERONE
method	X-RAY DIFFRACTION

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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	64.40 Å
rg_electron	63.24 Å
i0	8556660000.00
molecular_weight	779960.0 kDa
excluded_volume	977690 Å³
envelope_volume	1566300 Å³
shell_volume	195490 Å³
envelope_diameter	189.8 Å
shell_rg	75.35 Å
envelope_rg	59.66 Å
shape_rg	63.28 Å
total_rg	63.31 Å
total_atoms	54470
n_residues	7341
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	63.68 Å
rg_real_error	0.60 Å
i0_real	8.5560e+09
i0_real_error	1.3270e+08
rg_reciprocal	65.01 Å
i0_reciprocal	8576000000.0000
total_estimate	0.8370
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	93.0 Å
skewness	-0.098
kurtosis	-0.539
angular_range	— – 0.1200 Å⁻¹
current_alpha	0.0000
highest_alpha	4180000000.0000
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: 0.967; Smooth: 0.001

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Chaperonin GroEL
formula_weight	57471.7 kDa
ec_number	5.6.1.7
src_method	nat
entity_count	7

Polymer

type	polypeptide(L)
strand_id	A,B,E,F,H,J,M
atom_count	54517

MAAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVAKAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAATEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLPKNDAADLGAAGGMGGMGGMGGMM

Entity 2 polymer

description	Chaperonin GroEL
formula_weight	57391.7 kDa
ec_number	5.6.1.7
src_method	nat
entity_count	7

Polymer

type	polypeptide(L)
strand_id	C,D,G,I,K,L,N

MAAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVAKAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAATEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLPKNDAADLGAAGGMGGMGGMGGMM

Entity 3 non-polymer

description	HEXANE-1,6-DIOL
formula_weight	118.2 kDa
src_method	syn
entity_count	23

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	7

Entity 5 non-polymer

description	BETA-MERCAPTOETHANOL
formula_weight	78.1 kDa
src_method	syn
entity_count	35

Entity 6 non-polymer

description	TRIS(HYDROXYETHYL)AMINOMETHANE
formula_weight	163.2 kDa
src_method	syn
entity_count	3

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	47

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6. Citations (1)

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length_a	135.835 Å
length_b	262.165 Å
length_c	284.411 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	28

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	3.200 Å
resolution_low	49.200 Å
r_factor	0.1980
r_work	0.1960
r_free	0.2362

fit	/app/data/saxs_computation/wb/9wbt/9wbt.fit
pddf	/app/data/pr_computation/wb/9wbt/9wbt.pr.out
profile	/app/data/saxs_computation/wb/9wbt/9wbt.dat

Crystal Structure of Escherichia coli GroEL with Magnesium Ions and a Phosphorylated Serine Residue-3.2A

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

Diffraction

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)