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9s6b

Aeropyrum pernix acylaminoacyl peptidase co-crystallized with meropenem.

Method: X-RAY DIFFRACTION D_max: 150.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s6b
deposition_date	2025-07-31
last_revision	2025-10-22
title	Aeropyrum pernix acylaminoacyl peptidase co-crystallized with meropenem.
keywords	serine protease, HbPG, ligand binding, 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	46.30 Å
rg_electron	45.81 Å
i0	801579000.00
molecular_weight	235910.0 kDa
excluded_volume	295620 Å³
envelope_volume	402320 Å³
shell_volume	72280 Å³
envelope_diameter	149.9 Å
shell_rg	51.05 Å
envelope_rg	44.70 Å
shape_rg	45.82 Å
total_rg	45.98 Å
total_atoms	16662
n_residues	2282
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	150.9 Å
rg_real	46.15 Å
rg_real_error	1.22 Å
i0_real	8.0160e+08
i0_real_error	1.3920e+07
rg_reciprocal	46.30 Å
i0_reciprocal	801700000.0000
total_estimate	0.8268
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	62.1 Å
skewness	0.168
kurtosis	-0.547
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	97210000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Acylamino-acid-releasing enzyme
formula_weight	63064.5 kDa
ec_number	3.4.19.1
mutation	D524A
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	16990

MRIIMPVEFSRIVRDVERLIAVEKYSLQGVVDGDKLLVVGFSEGSVNAYLYDGGETVKLNREPINSVLDPHYGVGRVILVRDVSKGAEQHALFKVNTSRPGEEQRLEAVKPMRILSGVDTGEAVVFTGATEDRVALYALDGGGLRELARLPGFGFVSDIRGDLIAGLGFFGGGRVSLFTSNLSSGGLRVFDSGEGSFSSASISPGMKVTAGLETAREARLVTVDPRDGSVEDLELPSKDFSSYRPTAITWLGYLPDGRLAVVARREGRSAVFIDGERVEAPQGNHGRVVLWRGKLVTSHTSLSTPPRIVSLPSGEPLLEGGLPEDLRRSIAGSRLVWVESFDGSRVPTYVLESGRAPTPGPTVVLVHGGPFAEDSDSWDTFAASLAAAGFHVVMPNYRGSTGYGEEWRLKIIGDPCGGELEDVSAAARWARESGLASELYIMGYSYGGYMTLCALTMKPGLFKAGVAGASVVDWEEMYELSDAAFRNFIEQLTGGSREIMRSRSPINHVDRIKEPLALIHPQNASRTPLKPLLRLMGELLARGKTFEAHIIPDAGHAINTMEDAVKILLPAVFFLATQRERR

Source

organism	Aeropyrum pernix K1
ncbi_taxonomy_id	272557
host_organism	Escherichia coli

Entity 2 non-polymer

description	(2R,2'R)-3,3'-oxydipropane-1,2-diol
formula_weight	166.2 kDa
src_method	nat
entity_count	3

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	251

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6. Citations (1)

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length_a	71.042 Å
length_b	98.283 Å
length_c	98.902 Å
angle_alpha	105.51 °
angle_beta	103.19 °
angle_gamma	100.39 °
z_pdb	4

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	2.300 Å
resolution_low	39.220 Å
r_factor	0.1974
r_work	0.1968
r_free	0.2286

fit	/app/data/saxs_computation/s6/9s6b/9s6b.fit
pddf	/app/data/pr_computation/s6/9s6b/9s6b.pr.out
profile	/app/data/saxs_computation/s6/9s6b/9s6b.dat

Aeropyrum pernix acylaminoacyl peptidase co-crystallized with meropenem.

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