SAXSdb — 9zkf

▼

1. Structure Basics

entry_id	9zkf
deposition_date	2025-12-06
last_revision	2025-12-17
title	Heme-containing Fungal Catalase
keywords	Catalase, Aspergillus, Heme, Iron, Metal binding, OXIDOREDUCTASE; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	29.78 Å
rg_electron	28.89 Å
i0	105488000.00
molecular_weight	79130.0 kDa
excluded_volume	98026 Å³
envelope_volume	128210 Å³
shell_volume	36844 Å³
envelope_diameter	105.8 Å
shell_rg	36.22 Å
envelope_rg	29.82 Å
shape_rg	28.86 Å
total_rg	29.69 Å
total_atoms	5587
n_residues	701
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

▼

3. P(r) Analysis (GNOM)

dmax	101.0 Å
rg_real	29.77 Å
rg_real_error	0.50 Å
i0_real	1.0550e+08
i0_real_error	1.4090e+06
rg_reciprocal	29.78 Å
i0_reciprocal	105500000.0000
total_estimate	0.8836
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	34.3 Å
skewness	0.350
kurtosis	-0.301
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0002
highest_alpha	23100000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.966

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (7)

Entity 1 polymer

description	Catalase
formula_weight	77572.9 kDa
ec_number	1.11.1.6
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6104

QEQDNAGDTIEVTEQPIDNTLYVNDTGSYMTTDFGTPISDQTSLKAGPRGPTLLEDFIFRQKLQRFDHERVPERVVHARGAGAYGTFKSYADWSNVTAADFLSANDKETPMFCRFSTVVGFRGSVDTARDVHGHACRFYTDEGNYDIVGINFAPFFIQDAIQFPDLVHAIKPMPNNEIPQAATAHTSAWDFFSQQSTALHSALWLMSGNGIPRSFRHMNGYGVHSFRFVAANGTSKVVRYRWKSQQGVASLVWDEAQAAAGKNSDYHRQDLYNAIANGHYPKYELQAQIMDEADMLRFGFDLLDPTKLVPEEVVPYTPLGMMELNANPTNYFAEVEQAGFQPGHVVPGIDFTDDPLLQGRLFSYLDTQLTRHGGPNFEQIPVNRPRKPVHNNNRDGFGQQQIPTNNWAYTPNSMSNGYPMQANQTQGHGFFTAPYRYASGHLVRQTSPTFNDHWSQPAMFWNSLIPAEQQMVVNAIVFENSKVNSPHVRKNVVNQLNMVNNNLAVRVARGLGLDEPSPNPTYYTSNKTSNVGTFGKPLLSIEGLQVGFLASNSHPESIKQGQAMAAQFSAAGVDLNIVTEAYADGVNTTYALSDAIDFDALIIADGVQSLFASPALANQMNSTATSTLYPPARPFQILVDSFRYGKPVAAVGSGSVALKNAGIDSSRSGVYTGSSETTEKIAKEVLEGLYTFRFVDRFALDE

Source

organism	Aspergillus niger
ncbi_taxonomy_id	5061
host_organism	Aspergillus niger

Entity 2 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	1

Entity 3 non-polymer

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

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	HYDROGEN PEROXIDE
formula_weight	34.0 kDa
src_method	syn
entity_count	3

Entity 6 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	517

▶

6. Citations (1)

▶

length_a	78.522 Å
length_b	112.096 Å
length_c	172.583 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 2 2 2
int_tables_number	23
crystal_system	—

resolution	1.821 Å
resolution_low	30.009 Å
r_factor	—
r_work	0.2021
r_free	0.2503

fit	/app/data/saxs_computation/zk/9zkf/9zkf.fit
pddf	/app/data/pr_computation/zk/9zkf/9zkf.pr.out
profile	/app/data/saxs_computation/zk/9zkf/9zkf.dat

Heme-containing Fungal Catalase

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction