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9qup

Tb(III)-bound de novo protein scaffold TFD-EE MPNN

Method: X-RAY DIFFRACTION D_max: 59.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qup
deposition_date	2025-04-10
title	Tb(III)-bound de novo protein scaffold TFD-EE MPNN
keywords	TIM barrel, Enzyme Engineering, Metal Coordination, Photoenzyme, ProteinMPNN, 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	20.33 Å
rg_electron	19.09 Å
i0	22930000.00
molecular_weight	37276.0 kDa
excluded_volume	47104 Å³
envelope_volume	54191 Å³
shell_volume	22924 Å³
envelope_diameter	59.5 Å
shell_rg	26.19 Å
envelope_rg	19.23 Å
shape_rg	19.10 Å
total_rg	20.03 Å
total_atoms	2608
n_residues	337
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	59.5 Å
rg_real	20.17 Å
rg_real_error	0.27 Å
i0_real	2.2930e+07
i0_real_error	2.6910e+05
rg_reciprocal	20.20 Å
i0_reciprocal	22930000.0000
total_estimate	0.9091
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	26.4 Å
skewness	0.067
kurtosis	-0.511
angular_range	— – 0.3900 Å⁻¹
current_alpha	0.0000
highest_alpha	10680000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.950; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.990

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	TFD-EE MPNN
formula_weight	18338.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	2653

MMTFIVWALNKDEMLKNIEALRKAGAKNIAVESGDFDILRAAIEAGVETIVVSGGGLTIVFTGADRAALRRAAKRLLDAALELGAVVTVALDGDALRVRITGVPEQDLERLRALARELAAEFGIEVEVRGGGTPERALREIQELRELGAKNIWVESANVDWLLKLLKLS

Source

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

Entity 2 non-polymer

description	TERBIUM(III) ION
formula_weight	158.9 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	3

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	45

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6. Citations (1)

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length_a	42.980 Å
length_b	66.440 Å
length_c	94.370 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.950 Å
resolution_low	30.000 Å
r_factor	0.1974
r_work	0.1959
r_free	0.2258

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