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9u78

Single Chain Protein of De Novo Designed Helix Bundles-4EH2 with KDPV Loop

Method: X-RAY DIFFRACTION D_max: 68.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u78
deposition_date	2025-03-24
title	Single Chain Protein of De Novo Designed Helix Bundles-4EH2 with KDPV Loop
keywords	De Novo Protein, Helix Bundles, Single Chain, Metalloprotein; DE NOVO 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	20.12 Å
rg_electron	19.61 Å
i0	13762700.00
molecular_weight	28525.0 kDa
excluded_volume	36006 Å³
envelope_volume	41388 Å³
shell_volume	18190 Å³
envelope_diameter	72.0 Å
shell_rg	25.37 Å
envelope_rg	19.87 Å
shape_rg	19.64 Å
total_rg	20.38 Å
total_atoms	2009
n_residues	236
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	68.4 Å
rg_real	20.13 Å
rg_real_error	0.33 Å
i0_real	1.3760e+07
i0_real_error	1.7000e+05
rg_reciprocal	20.14 Å
i0_reciprocal	13760000.0000
total_estimate	0.6311
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	19.5 Å
skewness	0.394
kurtosis	-0.236
angular_range	— – 0.3950 Å⁻¹
current_alpha	0.0086
highest_alpha	7490000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.743; Stabil: 0.999; Sysdev: 0.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Single Chain Protein of De Novo Designed Helix Bundles-4EH2 with KDPV Loop
formula_weight	14332.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	2295

GGIEELLRKIIEDEVRHIAELEDIEKWLKDPVIEELLRKIIEDEVRHIAELEDIEKWLKDPVIEELLRKIIEDEVRHIAELEDIEKWLKDPVIEELLRKIIEDEVRHIAELEDIEKWL

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	nat
entity_count	2

Entity 4 non-polymer

description	FORMIC ACID
formula_weight	46.0 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	197

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6. Citations (1)

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length_a	50.748 Å
length_b	69.748 Å
length_c	55.048 Å
angle_alpha	90.00 °
angle_beta	104.80 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.700 Å
resolution_low	49.060 Å
r_factor	0.1776
r_work	0.1765
r_free	0.1988

fit	/app/data/saxs_computation/u7/9u78/9u78.fit
pddf	/app/data/pr_computation/u7/9u78/9u78.pr.out
profile	/app/data/saxs_computation/u7/9u78/9u78.dat