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9uew

Wild-type Bacillus megaterium Penicillin G Acylase with Non-Covalently Bound Phenylacetic Acid

Method: X-RAY DIFFRACTION D_max: 85.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uew
deposition_date	2025-04-09
last_revision	2026-02-18
title	Wild-type Bacillus megaterium Penicillin G Acylase with Non-Covalently Bound Phenylacetic Acid
keywords	;N-terminal nucleophile hydrolase, Bacillus megaterium, penicillin acylase, nob-covalently bound PAA, enzyme-product complex, 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	27.66 Å
rg_electron	26.67 Å
i0	115846000.00
molecular_weight	85454.0 kDa
excluded_volume	106980 Å³
envelope_volume	124560 Å³
shell_volume	37431 Å³
envelope_diameter	91.2 Å
shell_rg	35.36 Å
envelope_rg	26.94 Å
shape_rg	26.62 Å
total_rg	27.69 Å
total_atoms	6019
n_residues	725
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	85.0 Å
rg_real	27.49 Å
rg_real_error	0.42 Å
i0_real	1.1580e+08
i0_real_error	1.7490e+06
rg_reciprocal	27.54 Å
i0_reciprocal	115900000.0000
total_estimate	0.9085
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	34.3 Å
skewness	0.157
kurtosis	-0.518
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	27280000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.986

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

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	6540

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	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	19

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	3

Entity 7 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

description	2-PHENYLACETIC ACID
formula_weight	136.1 kDa
src_method	syn
entity_count	1

Entity 9 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	505

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6. Citations (1)

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length_a	57.995 Å
length_b	76.951 Å
length_c	82.216 Å
angle_alpha	90.00 °
angle_beta	100.47 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.960 Å
resolution_low	28.570 Å
r_factor	0.1440
r_work	0.1416
r_free	0.1877

fit	/app/data/saxs_computation/ue/9uew/9uew.fit
pddf	/app/data/pr_computation/ue/9uew/9uew.pr.out
profile	/app/data/saxs_computation/ue/9uew/9uew.dat

Wild-type Bacillus megaterium Penicillin G Acylase with Non-Covalently Bound Phenylacetic Acid

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 (10)

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 non-polymer

Entity 9 non-polymer

Entity 10 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)