← Back to search

9qph

Isopenicillin N synthase in complex with Fe and IPN using tr-SFX

Method: X-RAY DIFFRACTION D_max: 64.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9qph
deposition_date	2025-03-27
last_revision	2026-04-08
title	Isopenicillin N synthase in complex with Fe and IPN using tr-SFX
keywords	Isopenicillin N synthase, IPNS, tr-SFX, XFEL, time-resolved crystallography, ADE tape drive, OXIDOREDUCTASE; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	20.62 Å
rg_electron	19.33 Å
i0	23590400.00
molecular_weight	36910.0 kDa
excluded_volume	45928 Å³
envelope_volume	52802 Å³
shell_volume	22317 Å³
envelope_diameter	66.9 Å
shell_rg	26.26 Å
envelope_rg	19.63 Å
shape_rg	19.33 Å
total_rg	20.24 Å
total_atoms	2613
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

▼

3. P(r) Analysis (GNOM)

dmax	64.6 Å
rg_real	20.49 Å
rg_real_error	0.30 Å
i0_real	2.3590e+07
i0_real_error	3.1250e+05
rg_reciprocal	20.51 Å
i0_reciprocal	23590000.0000
total_estimate	0.8958
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.2 Å
skewness	0.141
kurtosis	-0.419
angular_range	— – 0.3850 Å⁻¹
current_alpha	0.0000
highest_alpha	5666000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.990

▶

4. Crystallography & Experiment

▶

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	2792

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	1

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	153

▶

6. Citations (1)

▶

length_a	41.915 Å
length_b	75.068 Å
length_c	101.855 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	1.700 Å
resolution_low	22.460 Å
r_factor	0.1903
r_work	0.1887
r_free	0.2171

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