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9ryg

Bifunctional Non-haem Iron Oxygenase NovR Involved in Novobiocin Biosynthesis with product bound

Method: X-RAY DIFFRACTION D_max: 90.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ryg
deposition_date	2025-07-15
last_revision	2025-07-23
title	Bifunctional Non-haem Iron Oxygenase NovR Involved in Novobiocin Biosynthesis with product bound
keywords	homotetramer, C4 symmetry, 3-dimethylallyl-4-hydroxybenzoate, LYASE; LYASE
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	29.89 Å
rg_electron	28.92 Å
i0	419600000.00
molecular_weight	108980.0 kDa
excluded_volume	104950 Å³
envelope_volume	171860 Å³
shell_volume	46912 Å³
envelope_diameter	91.3 Å
shell_rg	38.28 Å
envelope_rg	28.87 Å
shape_rg	28.89 Å
total_rg	29.55 Å
total_atoms	8267
n_residues	1030
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	90.4 Å
rg_real	29.70 Å
rg_real_error	0.37 Å
i0_real	4.1960e+08
i0_real_error	5.6400e+06
rg_reciprocal	29.78 Å
i0_reciprocal	419600000.0000
total_estimate	0.7046
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	39.2 Å
skewness	0.111
kurtosis	-0.540
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	116200000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 0.135; Positv: 1.000; Valcen: 0.980; Smooth: 0.939

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Decarboxylase NovR
formula_weight	30562.4 kDa
ec_number	4.1.-.-
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	9253

DHPFTMSEALANMPGDDYFRQPPVFDTYAEHRAYLKFRHAVALRHFARLGFDQDGLAGLITVADPEHADTYWANPLAHPFSTITPADLIRVDGDSAETVEGQRRVNIAAFNIHAEIHRARPDVQAVIHLHTVYGRAFSAFARKLPPLTQDACPFFEDHEVFDDFTGLVLAKDDGRRIAKQLRGHKAILLKNHGLVTVGETLDAAAWWFTLLDTCCHVQLLADAAGKPEEIPAEVARLTGRQLGSHLLGWNSYQPLHEAALARDPDLATMEPALPS

Source

organism	Streptomyces niveus
ncbi_taxonomy_id	193462
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	3-(3-methylbut-2-enyl)-4-oxidanyl-benzoic acid
formula_weight	206.2 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	6

Entity 5 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	15

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	883

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6. Citations (1)

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length_a	86.508 Å
length_b	138.968 Å
length_c	100.615 Å
angle_alpha	90.00 °
angle_beta	101.44 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.791 Å
resolution_low	49.356 Å
r_factor	—
r_work	0.1608
r_free	0.1883

fit	/app/data/saxs_computation/ry/9ryg/9ryg.fit
pddf	/app/data/pr_computation/ry/9ryg/9ryg.pr.out
profile	/app/data/saxs_computation/ry/9ryg/9ryg.dat