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9wvo

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

Method: X-RAY DIFFRACTION D_max: 55.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wvo
deposition_date	2025-09-21
last_revision	2026-02-11
title	crystal structure of retro-aldolase RA95.5-8 mutant 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	18.33 Å
rg_electron	17.22 Å
i0	25323300.00
molecular_weight	25860.0 kDa
excluded_volume	25042 Å³
envelope_volume	40034 Å³
shell_volume	18917 Å³
envelope_diameter	55.8 Å
shell_rg	23.94 Å
envelope_rg	17.45 Å
shape_rg	17.18 Å
total_rg	18.03 Å
total_atoms	1961
n_residues	238
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	55.4 Å
rg_real	18.18 Å
rg_real_error	0.21 Å
i0_real	2.5320e+07
i0_real_error	2.5440e+05
rg_reciprocal	18.20 Å
i0_reciprocal	25320000.0000
total_estimate	0.9019
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	24.7 Å
skewness	0.056
kurtosis	-0.511
angular_range	— – 0.4350 Å⁻¹
current_alpha	0.0000
highest_alpha	8227000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.995

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	retro-aldolase
formula_weight	29990.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2208

MPRYLKGWLEDVVQLSLRRPSVHASRQRPIISLNERILEFNKRNITAIIAYYLRKSPSGLDVERDPIEYAKYMERYAVGLSIXTEEKYFNGSYEMLRKIASSVSIPILMNDFIVKESQIDDAYNLGADTVALIVAILTERELESLLEYARSYGMEPLILINDENDLDIALRIGARFIVIFSMNAETGEINKENQRKLISMIPSNVVKVAHLDISERNEIEELRKLGVNAFLISSSLMRNPEKIKELIEGSLEHHHHHH

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	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	196

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6. Citations (1)

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length_a	62.654 Å
length_b	68.989 Å
length_c	68.046 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	1.660 Å
resolution_low	48.450 Å
r_factor	0.1749
r_work	0.1735
r_free	0.2037

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

crystal structure of retro-aldolase RA95.5-8 mutant 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