← Back to search

9yys

Crystal Structure of the Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl10 at Cryo Temperature

Method: X-RAY DIFFRACTION D_max: 119.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9yys
deposition_date	2025-10-29
title	Crystal Structure of the Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl10 at Cryo Temperature
keywords	Nylon hydrolase, amidase, Ntn-hydrolase, amide bond hydrolase, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	36.62 Å
rg_electron	35.88 Å
i0	446311000.00
molecular_weight	164900.0 kDa
excluded_volume	203890 Å³
envelope_volume	248830 Å³
shell_volume	56465 Å³
envelope_diameter	119.2 Å
shell_rg	43.35 Å
envelope_rg	35.55 Å
shape_rg	35.90 Å
total_rg	36.25 Å
total_atoms	11603
n_residues	1639
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

▼

3. P(r) Analysis (GNOM)

dmax	119.0 Å
rg_real	36.54 Å
rg_real_error	0.78 Å
i0_real	4.4630e+08
i0_real_error	7.4950e+06
rg_reciprocal	36.59 Å
i0_reciprocal	446300000.0000
total_estimate	0.8970
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	44.3 Å
skewness	0.256
kurtosis	-0.494
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	135200000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.936

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	L-aminopeptidase/D-esterase
formula_weight	28916.5 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	12497

MTAFGVDGVRVGHWSDPDAATGCTVVELPPGTVASYEVRGGAPASRELIALEPDKSVTAVDAVLLTGGSAFGLAAADGVMRRLEEAGRGVTTPAGVVPIVAAMALYDLAAGDASVRPGPAEGYAAARDVGTDVALHGRIGAGTGAHVGNWRGVDGRRPGGLGHAVRRLDDVVVAALCAVNAFGDIDDGHDEVVLDALRALPRPFDFERTNTTIGVVVTNARLDKTACRTVAQGAHDGLARAITPPHTRVDGDGFVAAATGEVEAHVDVVRLLALAAVTAAIRSVA

Source

organism	Jatrophihabitans endophyticus
ncbi_taxonomy_id	1206085
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	PYRUVIC ACID
formula_weight	88.1 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	D-MALATE
formula_weight	134.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	775

▶

6. Citations (1)

▶

length_a	83.126 Å
length_b	120.193 Å
length_c	148.305 Å
angle_alpha	90.00 °
angle_beta	92.99 °
angle_gamma	90.00 °
z_pdb	24

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.300 Å
resolution_low	68.400 Å
r_factor	0.1439
r_work	0.1425
r_free	0.1701

fit	/app/data/saxs_computation/yy/9yys/9yys.fit
pddf	/app/data/pr_computation/yy/9yys/9yys.pr.out
profile	/app/data/saxs_computation/yy/9yys/9yys.dat