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9qpi

Isopenicillin N synthase in complex with Fe and ACV

Method: X-RAY DIFFRACTION D_max: 65.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qpi
deposition_date	2025-03-27
last_revision	2026-04-08
title	Isopenicillin N synthase in complex with Fe and ACV
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	20.77 Å
rg_electron	19.40 Å
i0	24588600.00
molecular_weight	37589.0 kDa
excluded_volume	46753 Å³
envelope_volume	53755 Å³
shell_volume	22574 Å³
envelope_diameter	66.8 Å
shell_rg	26.40 Å
envelope_rg	19.75 Å
shape_rg	19.39 Å
total_rg	20.33 Å
total_atoms	2657
n_residues	329
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	65.4 Å
rg_real	20.63 Å
rg_real_error	0.44 Å
i0_real	2.4590e+07
i0_real_error	3.2830e+05
rg_reciprocal	20.66 Å
i0_reciprocal	24590000.0000
total_estimate	0.8147
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	27.5 Å
skewness	0.140
kurtosis	-0.419
angular_range	— – 0.3850 Å⁻¹
current_alpha	0.0000
highest_alpha	6013000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.000

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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	2972

MGSVSKANVPKIDVSPLFGDDQAAKMRVAQQIDAASRDTGFFYAVNHGINVQRLSQKTKEFHMSITPEEKWDLAIRAYNKEHQDQVRAGYYLSIPGKKAVESFCYLNPNFTPDHPRIQAKTPTHEVNVWPDETKHPGFQDFAEQYYWDVFGLSSALLKGYALALGKEENFFARHFKPDDTLASVVLIRYPYLDPYPEAAIKTAADGTKLSFEWHEDVSLITVLYQSNVQNLQVETAAGYQDIEADDTGYLINCGSYMAHLTNNYYKAPIHRVKWVNAERQSLPFFVNLGYDSVIDPFDPREPNGKSDREPLSYGDYLQNGLVSLINKNGQT

Source

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

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

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

Entity 4 non-polymer

description	L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE
formula_weight	363.4 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	227

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6. Citations (1)

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length_a	41.834 Å
length_b	75.521 Å
length_c	101.806 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	orthorhombic

resolution	1.450 Å
resolution_low	22.570 Å
r_factor	0.1533
r_work	0.1525
r_free	0.1757

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