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9t0l

Catalase CryoEM Structure from Rhizobium radiobacter at 1.7A resolution

Method: ELECTRON MICROSCOPY D_max: 86.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t0l
deposition_date	2025-10-17
title	Catalase CryoEM Structure from Rhizobium radiobacter at 1.7A resolution
keywords	Catalase, NADPH, PROTOPORPHYRIN IX CONTAINING FE, 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	25.65 Å
rg_electron	24.79 Å
i0	55277700.00
molecular_weight	55231.0 kDa
excluded_volume	67786 Å³
envelope_volume	87165 Å³
shell_volume	29450 Å³
envelope_diameter	90.0 Å
shell_rg	31.77 Å
envelope_rg	25.93 Å
shape_rg	24.77 Å
total_rg	25.57 Å
total_atoms	7414
n_residues	480
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	86.0 Å
rg_real	25.68 Å
rg_real_error	0.52 Å
i0_real	5.5280e+07
i0_real_error	8.4070e+05
rg_reciprocal	25.67 Å
i0_reciprocal	55280000.0000
total_estimate	0.8735
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	29.1 Å
skewness	0.461
kurtosis	-0.085
angular_range	— – 0.3100 Å⁻¹
current_alpha	0.0001
highest_alpha	8343000.0000
n_real_points	63
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.795; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.970

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Catalase
formula_weight	55132.0 kDa
ec_number	1.11.1.6
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8122

MTDMNKKQGGTGSTTGTGAPAVSDRNSLTVGPDGPILLHDVHFLEQMAHFNREKVPERQPHAKGSGAFGTFETTHDVSAYTKAALFQKGATTEMLARFSTVAGEMGSPDTWRDVRGFSLKFYTDEGNYDLVGNNTPIFFVRDPMKFPHFIRSQKRLPDSGLRDNHMQWDFWTNNPESAHQVTYLMGVRGLPRTWRHMNGYGSHTYMWVNEAGERFWVKYHFHTHQGMEFFTNEEAGAMAGADADFHRRDLFDAIARGEHPAWTMSVQVMPYEEGKTYHINPFDLTKTWPHADYPLIEVGKMTLNRNPENFFAQIEQAAFSPGNTVPGIGLSPDKMLLGRAFAYNDAQRNRIGTNFHQLPVNQPKVPVNTYMFDGQMAYHHSGSAPVHATNSGGRSWSDETGAVHDGWEADGDFVRSAYTLRPGDDDFSQPGKLVREVFNDDERRQLVETVSGALLGGVRSPVLERAFDYWKSVDAEVGQRIEDAVRAGQAG

Source

organism	Agrobacterium radiobacter
ncbi_taxonomy_id	362
host_organism	Escherichia coli

Entity 2 non-polymer

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

Entity 3 non-polymer

description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
formula_weight	745.4 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	425

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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	1.73 Å
resolution_method	—
num_particles	990333

fit	/app/data/saxs_computation/t0/9t0l/9t0l.fit
pddf	/app/data/pr_computation/t0/9t0l/9t0l.pr.out
profile	/app/data/saxs_computation/t0/9t0l/9t0l.dat