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9yvv

Cocrystallized structure of Bmp7 in complex with 2,4-dibromophenol

Method: X-RAY DIFFRACTION D_max: 72.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yvv
deposition_date	2025-10-23
title	Cocrystallized structure of Bmp7 in complex with 2,4-dibromophenol
keywords	cytochrome P450 enzyme, biaryl coupling, 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	23.60 Å
rg_electron	22.32 Å
i0	50674200.00
molecular_weight	55219.0 kDa
excluded_volume	68887 Å³
envelope_volume	78662 Å³
shell_volume	28447 Å³
envelope_diameter	74.0 Å
shell_rg	30.18 Å
envelope_rg	22.64 Å
shape_rg	22.35 Å
total_rg	23.12 Å
total_atoms	3879
n_residues	472
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	72.5 Å
rg_real	23.45 Å
rg_real_error	0.33 Å
i0_real	5.0670e+07
i0_real_error	5.8500e+05
rg_reciprocal	23.49 Å
i0_reciprocal	50680000.0000
total_estimate	0.9069
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	29.4 Å
skewness	0.132
kurtosis	-0.528
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	10580000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.998

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Polybrominated aromatic compounds synthase
formula_weight	56486.4 kDa
ec_number	1.14.19.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4108

MRYYEEDANVTDSPNRNAAPKLIPTIKLGSQDNHDMMWNEDFHLTITNMAKKYGAIYALETGKTTLIALNDHNAVREALVNQSDVFNIRADLEILQVAPQKHFLELEAGELWSLHRKTFATAMRDYFRDRWDTMDQWLVTEIDDIEAAWKSQGDQAVFDPNRDISIKLASFLHRVMFDRRFGEFEESVFDEKSLSWLPAGFINSTRYELMPEHNKESYYAHYGDVIEKFASNLNGLDAYVSMNVLKEKECYNKGQYRHLTDFLLNACDDIPNDVKQQVGATEKEIIIGSLTQVAGAGGGVGAFALRWMLLYLASFPEKQKQVHAELDQVIGQNETPQQSHKGDLHYTQAFIAEVLRHCSITSMPASNYAASKDTFIDGYFVAKGTPLIVNNYGMTRDEALWENPDEFIPERFLEADGTFSKKQQAKSFPFGIGQRRCLGELFGKFLINTLFTHLAHRFEFSLPNNEPINLRAISGVFLVPEKVDIKAKSRSLSDS

Source

organism	Marinomonas mediterranea
ncbi_taxonomy_id	119864
host_organism	Escherichia coli

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

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

Entity 5 non-polymer

description	2,4-bis(bromanyl)phenol
formula_weight	251.9 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	220

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6. Citations (1)

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length_a	101.220 Å
length_b	101.220 Å
length_c	159.924 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32 2 1
int_tables_number	154
crystal_system	—

resolution	2.320 Å
resolution_low	45.550 Å
r_factor	0.1946
r_work	0.1927
r_free	0.2304

fit	/app/data/saxs_computation/yv/9yvv/9yvv.fit
pddf	/app/data/pr_computation/yv/9yvv/9yvv.pr.out
profile	/app/data/saxs_computation/yv/9yvv/9yvv.dat