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9qn3

Fe(II)-2-oxoglutarate-dependent pseudomonal iron uptake factor C in complex with 10 mM 2-oxoglutarate (Mn)

Method: X-RAY DIFFRACTION D_max: 102.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qn3
deposition_date	2025-03-24
last_revision	2026-04-08
title	Fe(II)-2-oxoglutarate-dependent pseudomonal iron uptake factor C in complex with 10 mM 2-oxoglutarate (Mn)
keywords	2-oxoglutrate, Iron transport, siderophore antibiotics, 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	34.04 Å
rg_electron	32.96 Å
i0	371760000.00
molecular_weight	154370.0 kDa
excluded_volume	192610 Å³
envelope_volume	233820 Å³
shell_volume	56666 Å³
envelope_diameter	106.3 Å
shell_rg	41.38 Å
envelope_rg	32.86 Å
shape_rg	32.98 Å
total_rg	33.47 Å
total_atoms	10902
n_residues	1350
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	102.9 Å
rg_real	33.83 Å
rg_real_error	0.59 Å
i0_real	3.7180e+08
i0_real_error	5.6250e+06
rg_reciprocal	33.97 Å
i0_reciprocal	371800000.0000
total_estimate	0.8969
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	46.0 Å
skewness	0.088
kurtosis	-0.471
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	435900000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.938

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	PKHD-type hydroxylase PiuC
formula_weight	26291.5 kDa
ec_number	1.14.11.-
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	12244

GGSGGGGGGSSGLLHIPAIFTAEEVSRIRAALEQAEWADGKATAGYQSAKAKHNLQLPQDHPLAREIGEAMLQRLWNHPLFMSAALPLKVFPPLFNCYTGGGSFDFHIDNAVRDVHGGRERVRTDLSSTLFFSDPEDYDGGELVIQDTYGLQQVKLPAGDLVLYPGTSLHKVNPVTRGARYASFFWTQSLVREDSQRTLLFEMDQSIQRLTRDVPDHPSLIRLTGTYHNLLRRWSEL

Source

organism	Pseudomonas aeruginosa
ncbi_taxonomy_id	287
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	2-OXOGLUTARIC ACID
formula_weight	146.1 kDa
src_method	nat
entity_count	6

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	963

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6. Citations (1)

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length_a	80.633 Å
length_b	80.685 Å
length_c	88.803 Å
angle_alpha	62.99 °
angle_beta	62.99 °
angle_gamma	59.98 °
z_pdb	6

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	1.900 Å
resolution_low	75.610 Å
r_factor	0.1728
r_work	0.1726
r_free	0.1848

fit	/app/data/saxs_computation/qn/9qn3/9qn3.fit
pddf	/app/data/pr_computation/qn/9qn3/9qn3.pr.out
profile	/app/data/saxs_computation/qn/9qn3/9qn3.dat