Lip3 DL-peptidase in the apo-state

Method: X-RAY DIFFRACTION D_max: 82.9 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9sn1
deposition_date	2025-09-09
title	Lip3 DL-peptidase in the apo-state
keywords	DL-Peptidase, Paenibacillus, Syringafactin, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	26.72 Å
rg_electron	25.76 Å
i0	85523000.00
molecular_weight	72155.0 kDa
excluded_volume	90023 Å³
envelope_volume	109370 Å³
shell_volume	34414 Å³
envelope_diameter	85.3 Å
shell_rg	34.12 Å
envelope_rg	25.74 Å
shape_rg	25.75 Å
total_rg	26.64 Å
total_atoms	10023
n_residues	663
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	82.9 Å
rg_real	26.56 Å
rg_real_error	0.44 Å
i0_real	8.5520e+07
i0_real_error	1.1260e+06
rg_reciprocal	26.61 Å
i0_reciprocal	85530000.0000
total_estimate	0.9055
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	35.1 Å
skewness	0.122
kurtosis	-0.519
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	26680000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.989

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

▶

6. Citations (1)

▶

length_a	97.410 Å
length_b	122.310 Å
length_c	143.130 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	2.040 Å
resolution_low	48.710 Å
r_factor	0.1984
r_work	0.1973
r_free	0.2257

description	Beta-lactamase family protein
formula_weight	72263.6 kDa
src_method	man
entity_count	1

type	polypeptide(L)
strand_id	A
atom_count	10396

Lip3 DL-peptidase in the apo-state

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	Paenibacillus
ncbi_taxonomy_id	44249
host_organism	Escherichia coli

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	287

fit	/app/data/saxs_computation/sn/9sn1/9sn1.fit
pddf	/app/data/pr_computation/sn/9sn1/9sn1.pr.out
profile	/app/data/saxs_computation/sn/9sn1/9sn1.dat