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9ppt

Ni- and Bi-bound structure of the H77C variant of TriCyt2

Method: X-RAY DIFFRACTION D_max: 62.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ppt
deposition_date	2025-07-21
last_revision	2025-10-22
title	Ni- and Bi-bound structure of the H77C variant of TriCyt2
keywords	Ni- and Bi-binding protein, assembly, METAL BINDING PROTEIN; METAL BINDING PROTEIN
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	20.44 Å
rg_electron	19.30 Å
i0	23353700.00
molecular_weight	35886.0 kDa
excluded_volume	44508 Å³
envelope_volume	51695 Å³
shell_volume	21802 Å³
envelope_diameter	67.3 Å
shell_rg	26.14 Å
envelope_rg	19.66 Å
shape_rg	19.29 Å
total_rg	20.23 Å
total_atoms	2502
n_residues	318
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	62.4 Å
rg_real	20.28 Å
rg_real_error	0.27 Å
i0_real	2.3350e+07
i0_real_error	3.0680e+05
rg_reciprocal	20.31 Å
i0_reciprocal	23350000.0000
total_estimate	0.8999
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.5 Å
skewness	0.032
kurtosis	-0.533
angular_range	— – 0.3900 Å⁻¹
current_alpha	0.0000
highest_alpha	7820000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.988

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Soluble cytochrome b562
formula_weight	11879.5 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	2917

ADWEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAKKATPPKLEDKSPASPEMIDFRVGFDILLWQIHDALCLANEGKVKEAQAAAEQLKTTVNAHWQKYR

Source

organism	Escherichia coli BL21(DE3)
ncbi_taxonomy_id	469008
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	Bismuth(III) ION
formula_weight	209.0 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	NICKEL (II) ION
formula_weight	58.7 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	369

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6. Citations (1)

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length_a	56.150 Å
length_b	70.540 Å
length_c	75.720 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	12

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.780 Å
resolution_low	45.100 Å
r_factor	0.2160
r_work	0.2123
r_free	0.2665

fit	/app/data/saxs_computation/pp/9ppt/9ppt.fit
pddf	/app/data/pr_computation/pp/9ppt/9ppt.pr.out
profile	/app/data/saxs_computation/pp/9ppt/9ppt.dat