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9wvz

crystal structure of retro-aldolase T53L/K210H RA95.5-8 with a covalently bound cyclohexenone derivative

Method: X-RAY DIFFRACTION D_max: 55.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wvz
deposition_date	2025-09-22
last_revision	2026-02-11
title	crystal structure of retro-aldolase T53L/K210H RA95.5-8 with a covalently bound cyclohexenone derivative
keywords	retro-aldolase, HYDROLASE; HYDROLASE
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	18.28 Å
rg_electron	17.16 Å
i0	26218600.00
molecular_weight	26378.0 kDa
excluded_volume	25543 Å³
envelope_volume	40575 Å³
shell_volume	19171 Å³
envelope_diameter	56.3 Å
shell_rg	24.01 Å
envelope_rg	17.39 Å
shape_rg	17.12 Å
total_rg	17.98 Å
total_atoms	2000
n_residues	239
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	55.8 Å
rg_real	18.14 Å
rg_real_error	0.23 Å
i0_real	2.6220e+07
i0_real_error	3.0050e+05
rg_reciprocal	18.16 Å
i0_reciprocal	26220000.0000
total_estimate	0.8984
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.1 Å
skewness	0.050
kurtosis	-0.509
angular_range	— – 0.4350 Å⁻¹
current_alpha	0.0000
highest_alpha	8969000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	retro-aldolase
formula_weight	30151.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2209

MPRYLKGWLEDVVQLSLRRPSVHASRQRPIISLNERILEFNKRNITAIIAYYLRKSPSGLDVERDPIEYAKYMERYAVGLSIXTEEKYFNGSYEMLRKIASSVSIPILMNDFIVKESQIDDAYNLGADTVLLIVNILTERELESLLEYARSYGMEPLILINDENDLDIALRIGARFIVIFSMNFETGEINKENQRKLISMIPSNVVKVAHLDISERNEIEELRKLGVNAFLISSSLMRNPEKIKELIEGSLEHHHHHH

Source

organism	Saccharolobus solfataricus
ncbi_taxonomy_id	2287
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 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	5

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	170

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6. Citations (1)

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length_a	62.750 Å
length_b	69.171 Å
length_c	69.510 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.790 Å
resolution_low	49.030 Å
r_factor	0.1761
r_work	0.1742
r_free	0.2123

fit	/app/data/saxs_computation/wv/9wvz/9wvz.fit
pddf	/app/data/pr_computation/wv/9wvz/9wvz.pr.out
profile	/app/data/saxs_computation/wv/9wvz/9wvz.dat

crystal structure of retro-aldolase T53L/K210H RA95.5-8 with a covalently bound cyclohexenone derivative

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