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9vgo

Crystal structure of the cytochrome P450 RosC in complexed with Rosamicin

Method: X-RAY DIFFRACTION D_max: 88.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vgo
deposition_date	2025-06-14
last_revision	2026-04-22
title	Crystal structure of the cytochrome P450 RosC in complexed with Rosamicin
keywords	Cytochrome P450, RosC, Multistep oxidation, Rosamicin, macrolide biosynthesis, 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	28.50 Å
rg_electron	27.56 Å
i0	243224000.00
molecular_weight	83920.0 kDa
excluded_volume	81663 Å³
envelope_volume	135090 Å³
shell_volume	39710 Å³
envelope_diameter	89.8 Å
shell_rg	35.94 Å
envelope_rg	27.47 Å
shape_rg	27.53 Å
total_rg	28.19 Å
total_atoms	6371
n_residues	770
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	88.4 Å
rg_real	28.35 Å
rg_real_error	0.45 Å
i0_real	2.4320e+08
i0_real_error	3.2470e+06
rg_reciprocal	28.40 Å
i0_reciprocal	243200000.0000
total_estimate	0.9000
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	34.7 Å
skewness	0.228
kurtosis	-0.440
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	52060000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.930

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Cytochrome P450
formula_weight	44052.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6763

GSHMGLLDWFAYMREHWPVSWDENRQAWHVFNYRDYLTVTTNPLIFSSDFSPAFPVPPELALLMGPGTIGGIDPPRHGPMRKLVSQAFTPRRIAQMEARIETITADILRQVRDQERIDIAADLAYPLPVTVIADMLGIPNEDHEKFREWVDIILSNEGLEYPNLPDDFTETVGPAIAEWSEFLYAQIAEKRARPQDDLMSGLLAVEVEGRKLTDEEVVNIVALLLTAGHISSATLLSNLFLVLEEHPEALAAVRADRSLVPGVVEETLRWRSPFNCIFRLLAQDTEIFGQPMRKGQMVIAWIASANRDTEVFTDPDTFDIRRESNKHLAFGYGIHHCLGAFLARQEAKVFLNQVLDEFSEFSIDHDGVEFYDPDQLTARRLPVQVVRG

Source

organism	Micromonospora rosaria
ncbi_taxonomy_id	47874
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	Rosamicin
formula_weight	581.7 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	D-MALATE
formula_weight	134.1 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

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

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	356

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6. Citations (1)

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length_a	127.640 Å
length_b	95.670 Å
length_c	95.910 Å
angle_alpha	90.00 °
angle_beta	109.07 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	2.300 Å
resolution_low	47.830 Å
r_factor	0.1950
r_work	0.1918
r_free	0.2552

fit	/app/data/saxs_computation/vg/9vgo/9vgo.fit
pddf	/app/data/pr_computation/vg/9vgo/9vgo.pr.out
profile	/app/data/saxs_computation/vg/9vgo/9vgo.dat