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9ykf

Crystal Structure of E. coli D23N YajL

Method: X-RAY DIFFRACTION D_max: 68.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ykf
deposition_date	2025-10-07
title	Crystal Structure of E. coli D23N YajL
keywords	DJ-1 superfamily, Cysteine dependent enzyme, HYDROLASE; HYDROLASE
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	21.86 Å
rg_electron	20.73 Å
i0	27947000.00
molecular_weight	41658.0 kDa
excluded_volume	52698 Å³
envelope_volume	59342 Å³
shell_volume	23585 Å³
envelope_diameter	69.5 Å
shell_rg	27.65 Å
envelope_rg	21.04 Å
shape_rg	20.75 Å
total_rg	21.57 Å
total_atoms	5915
n_residues	389
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	68.8 Å
rg_real	21.79 Å
rg_real_error	0.29 Å
i0_real	2.7950e+07
i0_real_error	3.1460e+05
rg_reciprocal	21.80 Å
i0_reciprocal	27950000.0000
total_estimate	0.7458
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	25.7 Å
skewness	0.297
kurtosis	-0.331
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0000
highest_alpha	6952000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 0.348; Positv: 1.000; Valcen: 1.000; Smooth: 0.971

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Protein/nucleic acid deglycase 3
formula_weight	21079.3 kDa
ec_number	3.1.2.-,3.5.1.-,3.5.1.124
mutation	D23N
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8008

GSHMSASALVCLAPGSEETEAVTTINLLVRGGIKVTTASVASDGNLAITCSRGVKLLADAPLVEVADGEYDVIVLPGGIKGAECFRDSTLLVETVKQFHRSGRIVAAICAAPATVLVPHDIFPIGNMTGFPTLKDKIPAEQWLDKRVVWDARVKLLTSQGPGTAIDFGLKIIDLLVGREKAHEVASQLVMAAGIYNYYE

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	nat
entity_count	6

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	nat
entity_count	5

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	nat
entity_count	3

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	576

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6. Citations (2)

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length_a	43.723 Å
length_b	78.335 Å
length_c	99.614 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	0.980 Å
resolution_low	39.170 Å
r_factor	0.0974
r_work	0.0969
r_free	0.1144

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