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9qud

Cu(II)-bound de novo protein scaffold TFD-EH

Method: X-RAY DIFFRACTION D_max: 55.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qud
deposition_date	2025-04-10
title	Cu(II)-bound de novo protein scaffold TFD-EH
keywords	TIM barrel, Enzyme Engineering, Metal Coordination, Conformational Dynamics, DE NOVO PROTEIN; 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	17.65 Å
rg_electron	16.80 Å
i0	6835480.00
molecular_weight	19285.0 kDa
excluded_volume	24337 Å³
envelope_volume	29262 Å³
shell_volume	14850 Å³
envelope_diameter	53.5 Å
shell_rg	22.44 Å
envelope_rg	17.13 Å
shape_rg	16.79 Å
total_rg	17.84 Å
total_atoms	1346
n_residues	170
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	55.0 Å
rg_real	17.59 Å
rg_real_error	0.29 Å
i0_real	6.8350e+06
i0_real_error	8.1170e+04
rg_reciprocal	17.60 Å
i0_reciprocal	6836000.0000
total_estimate	0.7732
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	21.3 Å
skewness	0.222
kurtosis	-0.513
angular_range	— – 0.4500 Å⁻¹
current_alpha	0.0000
highest_alpha	1917000.0000
n_real_points	76
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 0.424; Positv: 1.000; Valcen: 0.999; Smooth: 0.999

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	TFD-EH
formula_weight	18916.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1423

GAMGDILIVWAKDVDEMLKQVEILRRLGAKQIAVESSDWRILQEALKKGGDILIVNGGGMTITFRGDDLEALLKAAIEMIKQALKFGATITLSLDGNDLNINITGVPEQVRKELAKEAERLAKEFGITVTRTGGGDVDEMLKQVEILRRLGAKQIAVHSDDWRILQEALKKG

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	COPPER (II) ION
formula_weight	63.5 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	IMIDAZOLE
formula_weight	69.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	77

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6. Citations (1)

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length_a	76.830 Å
length_b	76.830 Å
length_c	70.010 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 31 2 1
int_tables_number	152
crystal_system	—

resolution	1.950 Å
resolution_low	30.000 Å
r_factor	0.1689
r_work	0.1663
r_free	0.2177

fit	/app/data/saxs_computation/qu/9qud/9qud.fit
pddf	/app/data/pr_computation/qu/9qud/9qud.pr.out
profile	/app/data/saxs_computation/qu/9qud/9qud.dat