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9pt3

Q108K:K40L:T51V:T53S:R58W:Y19W:L117E mutant of hCRBPII bound to fluorophore TD-1V-9

Method: X-RAY DIFFRACTION D_max: 88.7 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pt3
deposition_date	2025-07-27
last_revision	2025-10-29
title	Q108K:K40L:T51V:T53S:R58W:Y19W:L117E mutant of hCRBPII bound to fluorophore TD-1V-9
keywords	human cellular retinol binding protein II, hCRBPII, fluorescent protein, engineered protein, RETINOL BINDING PROTEIN; RETINOL BINDING 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	28.59 Å
rg_electron	27.84 Å
i0	124756000.00
molecular_weight	59201.0 kDa
excluded_volume	57371 Å³
envelope_volume	98920 Å³
shell_volume	29602 Å³
envelope_diameter	91.9 Å
shell_rg	35.11 Å
envelope_rg	27.41 Å
shape_rg	27.83 Å
total_rg	28.41 Å
total_atoms	4490
n_residues	532
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	88.7 Å
rg_real	28.51 Å
rg_real_error	0.50 Å
i0_real	1.2480e+08
i0_real_error	1.6200e+06
rg_reciprocal	28.55 Å
i0_reciprocal	124800000.0000
total_estimate	0.9083
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	40.3 Å
skewness	0.148
kurtosis	-0.646
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	35030000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.956; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.949

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Retinol-binding protein 2
formula_weight	15634.5 kDa
mutation	Q108K:K40L:T51V:T53S:R58W:Y19W:L117E
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	4827

TRDQNGTWEMESNENFEGWMKALDIDFATRKIAVRLTQTLVIDQDGDNFKVKSTSTFWNYDVDFTVGVEFDEYTKSLDNRHVKALVTWEGDVLVCVQKGEKENRGWKKWIEGDKLYEELTCGDQVCRQVFKKK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	(2E)-3-[4'-(dimethylamino)[1,1'-biphenyl]-4-yl]but-2-enal
formula_weight	265.4 kDa
src_method	syn
entity_count	4

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	330

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6. Citations (1)

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length_a	29.405 Å
length_b	66.742 Å
length_c	64.217 Å
angle_alpha	89.73 °
angle_beta	90.28 °
angle_gamma	90.10 °
z_pdb	4

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	1.790 Å
resolution_low	33.370 Å
r_factor	0.2201
r_work	0.2184
r_free	0.2552

fit	/app/data/saxs_computation/pt/9pt3/9pt3.fit
pddf	/app/data/pr_computation/pt/9pt3/9pt3.pr.out
profile	/app/data/saxs_computation/pt/9pt3/9pt3.dat

Q108K:K40L:T51V:T53S:R58W:Y19W:L117E mutant of hCRBPII bound to fluorophore TD-1V-9

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction