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9quo

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

Method: X-RAY DIFFRACTION D_max: 55.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9quo
deposition_date	2025-04-10
title	Co(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

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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	17.64 Å
rg_electron	16.82 Å
i0	6784990.00
molecular_weight	19277.0 kDa
excluded_volume	24338 Å³
envelope_volume	29117 Å³
shell_volume	14801 Å³
envelope_diameter	53.8 Å
shell_rg	22.36 Å
envelope_rg	17.13 Å
shape_rg	16.79 Å
total_rg	17.85 Å
total_atoms	1348
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	55.5 Å
rg_real	17.58 Å
rg_real_error	0.28 Å
i0_real	6.7850e+06
i0_real_error	7.1270e+04
rg_reciprocal	17.58 Å
i0_reciprocal	6785000.0000
total_estimate	0.8977
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	20.7 Å
skewness	0.227
kurtosis	-0.505
angular_range	— – 0.4500 Å⁻¹
current_alpha	0.0000
highest_alpha	1857000.0000
n_real_points	76
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.923

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4. Crystallography & Experiment

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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	1392

GAMGDILIVWAKDVDEMLKQVEILRRLGAKQIAVESSDWRILQEALKKGGDILIVNGGGMTITFRGDDLEALLKAAIEMIKQALKFGATIELSLDGNDLNINITGVPEQVRKELAKEAERLAKEFGITVTRTGGGDVDEMLKQVEILRRLGAKQIAVHSDDWRILQEALKKG

Source

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

Entity 2 non-polymer

description	COBALT (II) ION
formula_weight	58.9 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	IMIDAZOLE
formula_weight	69.1 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	44

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6. Citations (1)

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length_a	76.360 Å
length_b	76.360 Å
length_c	70.810 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	0.1913
r_work	0.1897
r_free	0.2194

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