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9wmb

crystal structure of a P450 BM3 heme domain mutant in complex with Zearalenone

Method: X-RAY DIFFRACTION D_max: 99.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wmb
deposition_date	2025-09-03
last_revision	2026-03-18
title	crystal structure of a P450 BM3 heme domain mutant in complex with Zearalenone
keywords	Heme, P450, Metal-binding, 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	31.79 Å
rg_electron	30.73 Å
i0	167203000.00
molecular_weight	105170.0 kDa
excluded_volume	132410 Å³
envelope_volume	162090 Å³
shell_volume	42992 Å³
envelope_diameter	106.1 Å
shell_rg	38.66 Å
envelope_rg	30.84 Å
shape_rg	30.73 Å
total_rg	31.38 Å
total_atoms	7418
n_residues	902
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	99.3 Å
rg_real	31.74 Å
rg_real_error	0.57 Å
i0_real	1.6720e+08
i0_real_error	2.6020e+06
rg_reciprocal	31.76 Å
i0_reciprocal	167200000.0000
total_estimate	0.8951
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.8 Å
skewness	0.303
kurtosis	-0.438
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	46780000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.843

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Bifunctional cytochrome P450/NADPH--P450 reductase
formula_weight	52146.3 kDa
ec_number	1.14.14.1,1.6.2.4
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8298

AIKEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGWVTRYLSSQRLIKEACDESRFDKNLWQALNFLREIQGDGLGLSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSTVRALDEAQNKLQRANPDDPAYDENKRQIQEDTKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEPLDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPL

Source

organism	Priestia megaterium (strain NBRC 15308)
ncbi_taxonomy_id	1348623
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	(3S,11E)-14,16-dihydroxy-3-methyl-3,4,5,6,9,10-hexahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione
formula_weight	318.4 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	759

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6. Citations (1)

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length_a	58.843 Å
length_b	145.286 Å
length_c	61.904 Å
angle_alpha	90.00 °
angle_beta	97.46 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.800 Å
resolution_low	24.760 Å
r_factor	0.1545
r_work	0.1529
r_free	0.1877

fit	/app/data/saxs_computation/wm/9wmb/9wmb.fit
pddf	/app/data/pr_computation/wm/9wmb/9wmb.pr.out
profile	/app/data/saxs_computation/wm/9wmb/9wmb.dat