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9t0m

Catalase cryoEM structure from Micrococcus luteus at 1.9 Angstrom resolution.

Method: ELECTRON MICROSCOPY D_max: 87.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t0m
deposition_date	2025-10-17
title	Catalase cryoEM structure from Micrococcus luteus at 1.9 Angstrom resolution.
keywords	Catalase, NADPH, Protoporphyrin IX, 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	26.17 Å
rg_electron	25.23 Å
i0	56820300.00
molecular_weight	55955.0 kDa
excluded_volume	68740 Å³
envelope_volume	89590 Å³
shell_volume	29858 Å³
envelope_diameter	90.0 Å
shell_rg	32.01 Å
envelope_rg	26.35 Å
shape_rg	25.20 Å
total_rg	26.01 Å
total_atoms	7549
n_residues	481
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	87.7 Å
rg_real	26.21 Å
rg_real_error	0.61 Å
i0_real	5.6820e+07
i0_real_error	7.9270e+05
rg_reciprocal	26.20 Å
i0_reciprocal	56820000.0000
total_estimate	0.8698
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.2 Å
skewness	0.466
kurtosis	-0.114
angular_range	— – 0.3050 Å⁻¹
current_alpha	0.0000
highest_alpha	8644000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.797; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.926

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Catalase
formula_weight	58098.8 kDa
ec_number	1.11.1.6
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8196

HHHHHHHHSGEHQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERRPHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFALRFYTEEGNYDLVGNNTPIFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAHQVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIAGENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISQKDYPRIKVGTLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLPVNRPKNAVHNYAFEGQMWYDHTGDRSTYVPNSNGDSWSDETGPVDDGWEADGTLTREAQALRADDDDFGQAGTLVREVFSDQERDDFVETVAGALKGVRQDVQARAFEYWKNVDATIGQRIEDEVKRHEGDGIPGVEAGGEARM

Source

organism	Micrococcus luteus
ncbi_taxonomy_id	1270
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	422

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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	1.90 Å
resolution_method	—
num_particles	261172

fit	/app/data/saxs_computation/t0/9t0m/9t0m.fit
pddf	/app/data/pr_computation/t0/9t0m/9t0m.pr.out
profile	/app/data/saxs_computation/t0/9t0m/9t0m.dat