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9wud

Cryo-EM structure of one-heme-missing self-sufficient P450 from Shimazuella soli

Method: ELECTRON MICROSCOPY D_max: 127.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wud
deposition_date	2025-09-18
title	Cryo-EM structure of one-heme-missing self-sufficient P450 from Shimazuella soli
keywords	self-sufficient P450, heme, oxidoreductase; OXIDOREDUCTASE
method	ELECTRON MICROSCOPY

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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	39.51 Å
rg_electron	38.84 Å
i0	510445000.00
molecular_weight	183090.0 kDa
excluded_volume	228400 Å³
envelope_volume	294300 Å³
shell_volume	61971 Å³
envelope_diameter	132.9 Å
shell_rg	45.70 Å
envelope_rg	38.41 Å
shape_rg	38.85 Å
total_rg	39.16 Å
total_atoms	12893
n_residues	1598
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	127.5 Å
rg_real	39.36 Å
rg_real_error	1.01 Å
i0_real	5.1040e+08
i0_real_error	8.6270e+06
rg_reciprocal	39.46 Å
i0_reciprocal	510500000.0000
total_estimate	0.8982
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	51.0 Å
skewness	0.195
kurtosis	-0.520
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	124600000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.916

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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	121038.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	12894

MDEANIIPQPKTYGPLGNIPLIDKDKPILSFMKLAEEYGPIFRLQTPGDSTIVVSGHELVKEVCDESRFLKSAEGPLEKVRAFGGDGLFTSWTHEPNWRKAHNILMPTFSQRAMKDYHDMMVDIAVQLIQKWIRLNPDETVDVPDDMTRLTLDTIGLCGFNYRFNSYYRETPHPFITSMVRALDEAMHQTQRLDLQDKLMIRTKRQFQHDIQVMFSLVDSIIAERRAGKNQKENDLLSRMLNVSDPETGEKLDDENIRYQIITFLIAGHETTSGLLSFALYFLLKNPDKLKKAYEEVDQVLTGSTPTYKQVLHLKYVRMILNEALRLWPTAPAFSLYAKEDTIIGGKYPVKKEQERITVLIPQLHRDKEAWGEDVEEFRPERFEDQNKVPHHAYKPFGNGQRACIGMQFALHEATLVLGMLLRHFEFIDYKDYQLDIKQTLTLKPGDFNIQVQPRNQPAFQQSVSVTEDVAAESKMEMKQVKDHFDQKSTIQGLNNRPLLVLYGSDTGTAEGIARELADTATLHGVHTEVATLNERIGELPKEGAVLIVTSSYNGKPPSNAGQFVQWLEAVQAGELSGVQYAVFGCGDHNWASTYQDVPRFIDKQLAEKGAVRFSARGEGDVSGDFEEQFDQWKEKMWSDAIEAFGLEISDDVKKDQNTLSLQFVKGTGGSPLARSYEAVYAKVVENRELQSPDSGRSTRHIEITLPKGVSYQEGDHLGVLPANSKENVHRVLQKYKLNENDQVVLTASGRSMAHLPLAQEVSLRDLLLYSVELQDAATRAQIRELAAFTVCPPHKRELEALLEEGIYQEQVLKKRISMLDLLEKYEACEMPFERFLELLHPLKPRYYSISSSPRLNSERASITVAVVRGPAWSGLGEYRGVASNYLADCKPGEDVMMFIRTPESNFQLPEESETPIIMVGPGTGLAPFRGFLQARDAMKQEGKTLGEAYLYFGCRNEADFIYRKELEQYKKNGIMTLYIAFSRKEGIPKTYVQHVMASNAESLIRILDQGGRLYICGDGSRMAPEVEATLKNSYQEVHGAGEQEASQWLEKLQKDGQYAKDVWAGL

Source

organism	Shimazuella soli
ncbi_taxonomy_id	1892854
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	FLAVIN MONONUCLEOTIDE
formula_weight	456.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	FLAVIN-ADENINE DINUCLEOTIDE
formula_weight	785.5 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.080 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.08 Å
resolution_method	—
num_particles	154436

fit	/app/data/saxs_computation/wu/9wud/9wud.fit
pddf	/app/data/pr_computation/wu/9wud/9wud.pr.out
profile	/app/data/saxs_computation/wu/9wud/9wud.dat