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9qq4

Mini-bacterioferritin from Candidatus Methanoperedens species BLZ2 as isolated form at 1.07-A resolution

Method: X-RAY DIFFRACTION D_max: 89.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qq4
deposition_date	2025-03-31
title	Mini-bacterioferritin from Candidatus Methanoperedens species BLZ2 as isolated form at 1.07-A resolution
keywords	;ferritin-like protein, mini-ferritin, Fe-coproporphyrin III, anaerobic methane-oxidising archaea, archaea, iron homeostasis, iron storage, dodecamer, nano-compartment, 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	28.82 Å
rg_electron	28.28 Å
i0	69499100.00
molecular_weight	65458.0 kDa
excluded_volume	81590 Å³
envelope_volume	100520 Å³
shell_volume	29200 Å³
envelope_diameter	95.5 Å
shell_rg	36.21 Å
envelope_rg	28.36 Å
shape_rg	28.28 Å
total_rg	28.99 Å
total_atoms	9064
n_residues	551
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	89.4 Å
rg_real	28.83 Å
rg_real_error	0.67 Å
i0_real	6.9500e+07
i0_real_error	1.0130e+06
rg_reciprocal	28.83 Å
i0_reciprocal	69500000.0000
total_estimate	0.7066
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	30.9 Å
skewness	0.247
kurtosis	-0.683
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	13020000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 0.156; Positv: 1.000; Valcen: 0.937; Smooth: 0.876

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Bacterioferritin
formula_weight	15969.1 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	10957

MSQKIIDALNKDREEELSAIIQYMKHHYEGEGMESPAILEIFKSIAKSEMDHAEKLGERIVYLGGTPTKKPEPIAEGGDLKKMVQDDLAKENHAIEQYKEHIKLAIEEDDPTTRLMLEEILSDEEDHADTWQTLLKVKK

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	nat
entity_count	8

Entity 3 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	8

Entity 4 non-polymer

description	1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX
formula_weight	708.5 kDa
src_method	nat
entity_count	4

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	nat
entity_count	4

Entity 6 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	4

Entity 7 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	924

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6. Citations (1)

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length_a	87.608 Å
length_b	87.608 Å
length_c	131.374 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	24

space_group	P 63
int_tables_number	173
crystal_system	—

resolution	1.070 Å
resolution_low	75.870 Å
r_factor	0.1087
r_work	0.1078
r_free	0.1254

fit	/app/data/saxs_computation/qq/9qq4/9qq4.fit
pddf	/app/data/pr_computation/qq/9qq4/9qq4.pr.out
profile	/app/data/saxs_computation/qq/9qq4/9qq4.dat