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9vgp

Crystal structure of the cytochrome P450 RosC in complexed with 20-dihydrorosamicin

Method: X-RAY DIFFRACTION D_max: 87.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vgp
deposition_date	2025-06-14
last_revision	2026-04-22
title	Crystal structure of the cytochrome P450 RosC in complexed with 20-dihydrorosamicin
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	28.37 Å
rg_electron	27.43 Å
i0	243332000.00
molecular_weight	83920.0 kDa
excluded_volume	81663 Å³
envelope_volume	134660 Å³
shell_volume	39724 Å³
envelope_diameter	90.3 Å
shell_rg	35.87 Å
envelope_rg	27.40 Å
shape_rg	27.40 Å
total_rg	28.07 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	87.6 Å
rg_real	28.23 Å
rg_real_error	0.46 Å
i0_real	2.4330e+08
i0_real_error	3.5140e+06
rg_reciprocal	28.28 Å
i0_reciprocal	243300000.0000
total_estimate	0.8990
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.4 Å
skewness	0.235
kurtosis	-0.427
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	58220000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.911

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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	6576

GSHMGLLDWFAYMREHWPVSWDENRQAWHVFNYRDYLTVTTNPLIFSSDFSPAFPVPPELALLMGPGTIGGIDPPRHGPMRKLVSQAFTPRRIAQMEARIETITADILRQVRDQERIDIAADLAYPLPVTVIADMLGIPNEDHEKFREWVDIILSNEGLEYPNLPDDFTETVGPAIAEWSEFLYAQIAEKRARPQDDLMSGLLAVEVEGRKLTDEEVVNIVALLLTAGHISSATLLSNLFLVLEEHPEALAAVRADRSLVPGVVEETLRWRSPFNCIFRLLAQDTEIFGQPMRKGQMVIAWIASANRDTEVFTDPDTFDIRRESNKHLAFGYGIHHCLGAFLARQEAKVFLNQVLDEFSEFSIDHDGVEFYDPDQLTARRLPVQVVRG

Source

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

Entity 2 non-polymer

description	20-dihydrorosamicin
formula_weight	583.8 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	205

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6. Citations (1)

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length_a	124.760 Å
length_b	95.310 Å
length_c	95.700 Å
angle_alpha	90.00 °
angle_beta	106.60 °
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	44.590 Å
r_factor	0.2197
r_work	0.2174
r_free	0.2625

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