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9qpg

Isopenicillin N synthase in complex with Fe and IPN

Method: X-RAY DIFFRACTION D_max: 64.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qpg
deposition_date	2025-03-27
last_revision	2026-04-08
title	Isopenicillin N synthase in complex with Fe and IPN
keywords	Isopenicillin N synthase, IPNS, tr-SFX, XFEL, time-resolved crystallography, ADE tape drive, OXIDOREDUCTASE; OXIDOREDUCTASE
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	20.58 Å
rg_electron	19.21 Å
i0	23845300.00
molecular_weight	37000.0 kDa
excluded_volume	45977 Å³
envelope_volume	52285 Å³
shell_volume	22180 Å³
envelope_diameter	67.0 Å
shell_rg	26.25 Å
envelope_rg	19.57 Å
shape_rg	19.20 Å
total_rg	20.16 Å
total_atoms	2616
n_residues	328
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	64.8 Å
rg_real	20.45 Å
rg_real_error	0.35 Å
i0_real	2.3850e+07
i0_real_error	2.9930e+05
rg_reciprocal	20.48 Å
i0_reciprocal	23850000.0000
total_estimate	0.8950
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.2 Å
skewness	0.142
kurtosis	-0.426
angular_range	— – 0.3850 Å⁻¹
current_alpha	0.0000
highest_alpha	5630000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.989

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Isopenicillin N synthase
formula_weight	37563.8 kDa
ec_number	1.21.3.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2943

MGSVSKANVPKIDVSPLFGDDQAAKMRVAQQIDAASRDTGFFYAVNHGINVQRLSQKTKEFHMSITPEEKWDLAIRAYNKEHQDQVRAGYYLSIPGKKAVESFCYLNPNFTPDHPRIQAKTPTHEVNVWPDETKHPGFQDFAEQYYWDVFGLSSALLKGYALALGKEENFFARHFKPDDTLASVVLIRYPYLDPYPEAAIKTAADGTKLSFEWHEDVSLITVLYQSNVQNLQVETAAGYQDIEADDTGYLINCGSYMAHLTNNYYKAPIHRVKWVNAERQSLPFFVNLGYDSVIDPFDPREPNGKSDREPLSYGDYLQNGLVSLINKNGQT

Source

organism	Aspergillus nidulans FGSC A4
ncbi_taxonomy_id	227321
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	ISOPENICILLIN N
formula_weight	359.4 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	265

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6. Citations (1)

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length_a	40.955 Å
length_b	74.098 Å
length_c	100.806 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.790 Å
resolution_low	59.700 Å
r_factor	0.1852
r_work	0.1826
r_free	0.2314

fit	/app/data/saxs_computation/qp/9qpg/9qpg.fit
pddf	/app/data/pr_computation/qp/9qpg/9qpg.pr.out
profile	/app/data/saxs_computation/qp/9qpg/9qpg.dat