SAXSdb — 9ub9

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1. Structure Basics

entry_id	9ub9
deposition_date	2025-04-02
last_revision	2026-02-18
title	Wild-type Bacillus megaterium Penicillin G Acylase
keywords	N-terminal nucleophile hydrolase, Bacillus megaterium, penicillin acylase, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
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	27.62 Å
rg_electron	26.64 Å
i0	111066000.00
molecular_weight	83831.0 kDa
excluded_volume	104990 Å³
envelope_volume	122850 Å³
shell_volume	36943 Å³
envelope_diameter	95.0 Å
shell_rg	35.29 Å
envelope_rg	26.89 Å
shape_rg	26.59 Å
total_rg	27.65 Å
total_atoms	5911
n_residues	716
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	87.8 Å
rg_real	27.45 Å
rg_real_error	0.55 Å
i0_real	1.1110e+08
i0_real_error	1.7540e+06
rg_reciprocal	27.50 Å
i0_reciprocal	111100000.0000
total_estimate	0.6873
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	35.4 Å
skewness	0.140
kurtosis	-0.531
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	25250000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 0.075; Positv: 1.000; Valcen: 0.995; Smooth: 0.987

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Penicillin G acylase
formula_weight	24452.5 kDa
ec_number	3.5.1.11
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6379

GEDKNEGVKVVRDNFGVPHLYAKNKKDLYEAYGYVMAKDRLFQLEMFRRGNEGTVSEIFGEDYLSKDEQSRRDGYSNKEIKKMIDGLDRQPKELIAKFAEGISRYVNEALKDPDDKLSKEFHEYQFLPQKWTSTDVVRVYMVSMTYFMDNHQELKNAEILAKLEHEYGTEVSRKMFDDLVWKNDPSAPTSIVSEGKPKRDSSSQSLQILS

Source

organism	Priestia megaterium
ncbi_taxonomy_id	1404
host_organism	Priestia megaterium

Entity 2 polymer

description	Penicillin G acylase subunit beta
formula_weight	61475.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

SNAAIVGSEKSATGNALLFSGPQVGFVAPGFLYEVGLHAPGFDMEGSGFIGYPFIMFGANNHFALSATAGYGNVTDIFEEKLNAKNSSQYLYKGKWRDMEKRKESFTVKGDNGEKKTVEKIYYRTVHGPVISRDETNKVAYSKSWSFRGTEAQSMSAYMKANWAKNLKEFENAASEYTMSLNWYYADKKGDIAYYHVGRYPVRNSKIDERIPTPGTGEYEWKGFIPFKENPHVINPKNGYVVNWNNKPSKEWVNGEYSFYWGEDNRVQQYINGMEARGKVTLEDINEINYTASFAQLRANLFKQLLIDVLDKNKSTNGNYIYLIEKLEEWNNLKEDENKDGYYDAGIAAFFDEWWNNLHDKLFMDELGDFYGITKEITDHRYGASLAYKILNKESTNYKWVNVDQEKIIMESTNEVLAKLQSEKGLKAEKWRMPIKTMTFGEKSLIGIPHGYGSMTPIIEMNRGSENHYIEMTPTGPSGFNITPPGQIGFVKKDGTISDHYDDQLVMFAEWKFKPYLFNKKDINKAAKNVSALNMSK

Source

organism	Priestia megaterium
ncbi_taxonomy_id	1404
host_organism	Priestia megaterium

Entity 3 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	5

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	5

Entity 6 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	440

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6. Citations (1)

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length_a	57.726 Å
length_b	77.475 Å
length_c	84.170 Å
angle_alpha	90.00 °
angle_beta	100.63 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.920 Å
resolution_low	30.940 Å
r_factor	0.1577
r_work	0.1557
r_free	0.1928

fit	/app/data/saxs_computation/ub/9ub9/9ub9.fit
pddf	/app/data/pr_computation/ub/9ub9/9ub9.pr.out
profile	/app/data/saxs_computation/ub/9ub9/9ub9.dat

Wild-type Bacillus megaterium Penicillin G Acylase

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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)