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9z0b

Crystal Structure of the Polycaprolactam (Nylon6) and Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl12 at Cryo Temperature

Method: X-RAY DIFFRACTION D_max: 136.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z0b
deposition_date	2025-10-31
last_revision	2026-06-03
title	Crystal Structure of the Polycaprolactam (Nylon6) and Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl12 at Cryo Temperature
keywords	Nylon hydrolase, amidase, Ntn-hydrolase, amide bond hydrolase, 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	44.31 Å
rg_electron	43.68 Å
i0	960643000.00
molecular_weight	266900.0 kDa
excluded_volume	338370 Å³
envelope_volume	440270 Å³
shell_volume	80864 Å³
envelope_diameter	142.3 Å
shell_rg	50.99 Å
envelope_rg	43.13 Å
shape_rg	43.67 Å
total_rg	44.03 Å
total_atoms	18862
n_residues	2484
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	136.8 Å
rg_real	44.02 Å
rg_real_error	1.16 Å
i0_real	9.6060e+08
i0_real_error	1.7320e+07
rg_reciprocal	44.31 Å
i0_reciprocal	961000000.0000
total_estimate	0.8974
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	60.8 Å
skewness	0.020
kurtosis	-0.585
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	129500000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.917

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Poly (caprolactam and hexamethylene adipamide) hydrolase Nyl12
formula_weight	35143.9 kDa
ec_number	3.5.1.117
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	19711

MAASSTDNILHFDFPEVQIGTAINPEGPTGITLFYFPKGVQASVDIQGGSVGTFFTQEKMQQGEAYLDGVAFTGGGILGLEAVAGAVSSLFADQTKNEVQFRRMPLISGAVIFDYTPRQNMIYPDKALGQKAFAALSAGQFVQGRHGAGVSASVGKLLRDGFQLAGQGGAFAQIGKTKIAVFTVVNAVGVILDEKGEVIYGLPKGATKQTLNQQVTELLQQPKKPFWPEPKNTTLTIVITNEKLAPRHLKQLGRQVHHALSQVIHPYATILDGDVLYTVSTRSIESDLYAPGADIESDLNAKFIYLGMVAGELAKQAVWSAVGYSHRP

Source

organism	Gammaproteobacteria bacterium
ncbi_taxonomy_id	1913989
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	CHOLINE ION
formula_weight	104.2 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
formula_weight	238.3 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	2

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	831

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6. Citations (1)

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length_a	119.623 Å
length_b	135.407 Å
length_c	142.882 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	32

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.750 Å
resolution_low	98.280 Å
r_factor	0.1629
r_work	0.1612
r_free	0.1965

fit	/app/data/saxs_computation/z0/9z0b/9z0b.fit
pddf	/app/data/pr_computation/z0/9z0b/9z0b.pr.out
profile	/app/data/saxs_computation/z0/9z0b/9z0b.dat