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13jg

E. coli DnaK bound to peptide PA1, structure B

Method: X-RAY DIFFRACTION D_max: 80.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	13jg
deposition_date	2026-05-09
last_revision	2026-05-27
title	E. coli DnaK bound to peptide PA1, structure B
keywords	allosteric inhibition, DnaK, molecular chaperones, peptidomimetics, proteotoxic stress, 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	21.57 Å
rg_electron	21.12 Å
i0	21922500.00
molecular_weight	23050.0 kDa
excluded_volume	21797 Å³
envelope_volume	38987 Å³
shell_volume	16493 Å³
envelope_diameter	82.1 Å
shell_rg	26.37 Å
envelope_rg	21.41 Å
shape_rg	21.10 Å
total_rg	21.70 Å
total_atoms	1734
n_residues	219
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	80.4 Å
rg_real	21.70 Å
rg_real_error	0.74 Å
i0_real	2.1920e+07
i0_real_error	3.3870e+05
rg_reciprocal	21.68 Å
i0_reciprocal	21920000.0000
total_estimate	0.8162
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	21.3 Å
skewness	0.474
kurtosis	-0.220
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	4026000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.670; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.616; Smooth: 0.982

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Chaperone protein DnaK
formula_weight	23820.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1978

VLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLMEIAQQQHA

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 non-polymer

description	peptide PA1-A
formula_weight	745.9 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	221

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6. Citations (1)

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length_a	37.900 Å
length_b	94.796 Å
length_c	117.444 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 2 2 2
int_tables_number	23
crystal_system	orthorhombic

resolution	1.520 Å
resolution_low	29.360 Å
r_factor	0.2088
r_work	0.2081
r_free	0.2220

fit	/app/data/saxs_computation/3j/13jg/13jg.fit
pddf	/app/data/pr_computation/3j/13jg/13jg.pr.out
profile	/app/data/saxs_computation/3j/13jg/13jg.dat

E. coli DnaK bound to peptide PA1, structure B

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