SAXSdb — 9qdt

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1. Structure Basics

entry_id	9qdt
deposition_date	2025-03-06
title	Cytochrome c peroxidase YhjA
keywords	cytochrome c, peroxidase, multiheme protein, 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	24.01 Å
rg_electron	23.34 Å
i0	39003800.00
molecular_weight	48635.0 kDa
excluded_volume	60892 Å³
envelope_volume	70923 Å³
shell_volume	25707 Å³
envelope_diameter	85.3 Å
shell_rg	30.29 Å
envelope_rg	23.69 Å
shape_rg	23.32 Å
total_rg	24.19 Å
total_atoms	3420
n_residues	417
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	82.8 Å
rg_real	24.02 Å
rg_real_error	0.65 Å
i0_real	3.9000e+07
i0_real_error	5.5530e+05
rg_reciprocal	24.02 Å
i0_reciprocal	39000000.0000
total_estimate	0.6557
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	27.1 Å
skewness	0.414
kurtosis	-0.163
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	11660000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.779; Stabil: 1.000; Sysdev: 0.101; Positv: 1.000; Valcen: 0.954; Smooth: 0.928

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Probable cytochrome c peroxidase
formula_weight	46412.3 kDa
ec_number	1.11.1.5
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3467

ENNKVLGFLREKGCDYCHTPSAELPAYYYIPGAKQLMDYDIKLGYKSFNLEAVRAALLADKPVSQSDLNKIEWVMQYETMPPTRYTALHWAGKVSDEERAEILAWIAKQRAEYYASNDTAPEHRNEPVQPIPQKLPTDAQKVALGFALYHDPRLSADSTISCAHCHALNAGGVDGRKTSIGVGGAVGPINAPTVFNSVFNVEQFWDGRAATLQDQAGGPPLNPIEMASKSWDEIIAKLEKDPQLKTQFLEVYPQGFSGENITDAIAEFEKTLITPDSPFDKWLRGDENALTAQQKKGYQLFKDNKCATCHGGIILGGRSFEPLGLKKDFNFGEITAADIGRMNVTKEERDKLRQKVPGLRNVALTAPYFHRGDVPTLDGAVKLMLRYQVGKELPQEDVDDIVAFLHSLNGVYTPYMQ

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	HEME C
formula_weight	618.5 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

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

Entity 4 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
formula_weight	238.3 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	nat
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	47

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6. Citations (1)

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length_a	101.420 Å
length_b	101.420 Å
length_c	134.680 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 41 21 2
int_tables_number	92
crystal_system	—

resolution	2.572 Å
resolution_low	81.149 Å
r_factor	—
r_work	0.1724
r_free	0.2219

fit	/app/data/saxs_computation/qd/9qdt/9qdt.fit
pddf	/app/data/pr_computation/qd/9qdt/9qdt.pr.out
profile	/app/data/saxs_computation/qd/9qdt/9qdt.dat

Cytochrome c peroxidase YhjA

SAXS Profile

P(r) Distribution