← Back to search

9qul

Zn(II)-bound de novo protein scaffold TFD-EH T87E

Method: X-RAY DIFFRACTION D_max: 54.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9qul
deposition_date	2025-04-10
title	Zn(II)-bound de novo protein scaffold TFD-EH T87E
keywords	TIM barrel, Enzyme Engineering, Metal Coordination, Conformational Dynamics, DE NOVO PROTEIN; DE NOVO PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	17.51 Å
rg_electron	16.66 Å
i0	6648880.00
molecular_weight	18963.0 kDa
excluded_volume	23915 Å³
envelope_volume	28345 Å³
shell_volume	14563 Å³
envelope_diameter	53.6 Å
shell_rg	22.09 Å
envelope_rg	16.92 Å
shape_rg	16.64 Å
total_rg	17.67 Å
total_atoms	1326
n_residues	169
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	54.3 Å
rg_real	17.44 Å
rg_real_error	0.27 Å
i0_real	6.6490e+06
i0_real_error	6.9080e+04
rg_reciprocal	17.45 Å
i0_reciprocal	6649000.0000
total_estimate	0.9062
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	21.0 Å
skewness	0.216
kurtosis	-0.518
angular_range	— – 0.4550 Å⁻¹
current_alpha	0.0000
highest_alpha	1878000.0000
n_real_points	76
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.980

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	TFD-EH T87E
formula_weight	18944.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1380

GAMGDILIVWAKDVDEMLKQVEILRRLGAKQIAVESSDWRILQEALKKGGDILIVNGGGMTITFRGDDLEALLKAAIEMIKQALKFGATIELSLDGNDLNINITGVPEQVRKELAKEAERLAKEFGITVTRTGGGDVDEMLKQVEILRRLGAKQIAVHSDDWRILQEALKKG

Source

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

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	IMIDAZOLE
formula_weight	69.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

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

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	54

▶

6. Citations (1)

▶

length_a	76.240 Å
length_b	76.240 Å
length_c	70.250 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	1.900 Å
resolution_low	30.000 Å
r_factor	0.1833
r_work	0.1815
r_free	0.2193

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