Crystal Structure of dehydratase ApmL in Amipurimycin biosynthesis

Method: X-RAY DIFFRACTION D_max: 72.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9x86
deposition_date	2025-10-18
title	Crystal Structure of dehydratase ApmL in Amipurimycin biosynthesis
keywords	DEHYDRATASE, LYASE; LYASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	21.83 Å
rg_electron	20.70 Å
i0	14816400.00
molecular_weight	28000.0 kDa
excluded_volume	34766 Å³
envelope_volume	46378 Å³
shell_volume	19389 Å³
envelope_diameter	73.4 Å
shell_rg	26.40 Å
envelope_rg	20.75 Å
shape_rg	20.67 Å
total_rg	21.64 Å
total_atoms	1980
n_residues	255
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	72.9 Å
rg_real	21.79 Å
rg_real_error	0.53 Å
i0_real	1.4820e+07
i0_real_error	2.1490e+05
rg_reciprocal	21.80 Å
i0_reciprocal	14820000.0000
total_estimate	0.8821
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.9 Å
skewness	0.289
kurtosis	-0.435
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0000
highest_alpha	4526000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.967

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

▶

6. Citations (1)

▶

length_a	103.840 Å
length_b	103.840 Å
length_c	130.922 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 61 2 2
int_tables_number	178
crystal_system	—

resolution	3.500 Å
resolution_low	42.530 Å
r_factor	0.2661
r_work	0.2625
r_free	0.3227

description	Amc20
formula_weight	33292.2 kDa
src_method	man
entity_count	1

type	polypeptide(L)
strand_id	A
atom_count	1981

Crystal Structure of dehydratase ApmL in Amipurimycin biosynthesis

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Streptomyces novoguineensis
ncbi_taxonomy_id	2586640
host_organism	Escherichia coli BL21(DE3)

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1

fit	/app/data/saxs_computation/x8/9x86/9x86.fit
pddf	/app/data/pr_computation/x8/9x86/9x86.pr.out
profile	/app/data/saxs_computation/x8/9x86/9x86.dat