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9si5

Crystal structure of DoxA in complex with reaction intermediate DHD

Method: X-RAY DIFFRACTION D_max: 100.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9si5
deposition_date	2025-08-28
title	Crystal structure of DoxA in complex with reaction intermediate DHD
keywords	P450, Oxygenase, reaction intermediate sanpshot, tetracyclin biosynthesis, TRANSFERASE; TRANSFERASE
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	31.45 Å
rg_electron	30.98 Å
i0	254707000.00
molecular_weight	84955.0 kDa
excluded_volume	81890 Å³
envelope_volume	137760 Å³
shell_volume	37377 Å³
envelope_diameter	108.8 Å
shell_rg	37.77 Å
envelope_rg	30.84 Å
shape_rg	30.97 Å
total_rg	31.40 Å
total_atoms	6449
n_residues	814
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	100.5 Å
rg_real	31.49 Å
rg_real_error	0.63 Å
i0_real	2.5470e+08
i0_real_error	3.8440e+06
rg_reciprocal	31.48 Å
i0_reciprocal	254700000.0000
total_estimate	0.8944
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.2 Å
skewness	0.345
kurtosis	-0.546
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	46110000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.901

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Cytochrome P-450 monooxygenase DoxA
formula_weight	49698.1 kDa
ec_number	1.14.13.181
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,D
atom_count	6585

MGGSHHHHHHGMASMTGGQQMGRDLYDDDDKDPSSRSGEAPRVAVDPFACPMMTMQRKPEVHDAFREAGPVVEVNAPAGGPAWVITDDALAREVLADPRFVKDPDLAPAAWRGVDDGLDIPVPELRPFTLIAVDGEAHRRLRRIHAPAFNPRRLAERTDRIAAIAGRLLTELADASGRSGKPAELIGGFAYHFPLLVICELLGVPVTDPAMAREAVSVLKALGLGGPQSGGGDGTDPAGGVPDTSALESLLLEAVHSARRNDTPTMTRVLYERAQAEFGSVSDDQLVYMITGLIFAGHDTTGSFLGFLLAEVLAGRLAADADEDAVSRFVEEALRYHPPVPYTLWRFAATEVTIGGVRLPRGAPVLVDIEGTNTDGRHHDAPHAFHPDRPSWRRLTFGDGPHYCIGEQLAQLESRTMIGVLRSRFPEARLAVPYDELRWCRKGAQTARLTELPVWLR

Source

organism	Streptomyces peucetius
ncbi_taxonomy_id	1950
host_organism	Escherichia coli

Entity 2 non-polymer

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

Entity 3 non-polymer

description	;(7~{S},9~{S})-7-[(2~{R},4~{S},5~{S},6~{S})-4-azanyl-6-methyl-5-oxidanyl-oxan-2-yl]oxy-4-methoxy-6,9,11-tris(oxidanyl)-9-[(1~{R})-1-oxidanylethyl]-8,10-dihydro-7~{H}-tetracene-5,12-dione ;
formula_weight	529.5 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	136

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6. Citations (1)

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length_a	101.873 Å
length_b	108.058 Å
length_c	179.772 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	2.540 Å
resolution_low	89.890 Å
r_factor	—
r_work	0.2335
r_free	0.2810

fit	/app/data/saxs_computation/si/9si5/9si5.fit
pddf	/app/data/pr_computation/si/9si5/9si5.pr.out
profile	/app/data/saxs_computation/si/9si5/9si5.dat

Crystal structure of DoxA in complex with reaction intermediate DHD

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction