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9wgn

Crystal structure of Orobanche cumana OcKAI2d2 covalently bound to KOK1007

Method: X-RAY DIFFRACTION D_max: 58.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wgn
deposition_date	2025-08-25
last_revision	2026-05-20
title	Crystal structure of Orobanche cumana OcKAI2d2 covalently bound to KOK1007
keywords	OcKAI2d2, enzyme, Orobanche cumana, triazole urea, KOK1007, 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	18.37 Å
rg_electron	17.36 Å
i0	28889700.00
molecular_weight	27417.0 kDa
excluded_volume	26383 Å³
envelope_volume	41532 Å³
shell_volume	19469 Å³
envelope_diameter	60.0 Å
shell_rg	24.26 Å
envelope_rg	17.62 Å
shape_rg	17.33 Å
total_rg	18.14 Å
total_atoms	2068
n_residues	267
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	58.5 Å
rg_real	18.23 Å
rg_real_error	0.19 Å
i0_real	2.8890e+07
i0_real_error	3.0160e+05
rg_reciprocal	18.26 Å
i0_reciprocal	28890000.0000
total_estimate	0.8863
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.7 Å
skewness	0.109
kurtosis	-0.421
angular_range	— – 0.4350 Å⁻¹
current_alpha	0.0002
highest_alpha	6853000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.999

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Alpha/beta-hydrolases superfamily protein
formula_weight	30318.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2309

GPLGSMGSIVGAAHNVRVMGSGQTTVVLGHGLGIDQSVWRHLVPRLVDHYKVVLYDNMGAGTTNPDKYDFNRYATLNGYADDLLAILEEFSVGKCIYVGHSFSAMVGAMASILRPDLFRKLIMIAATPRMSNTEDYYGGLNQEDVDQLLYGLETNYNSMAHGMAPLVVGGDMDSEVVQEYSRTLFNMRPDIALSVARMINSYDMRPFLGSVVVPCHIIHSCKDHAVPVTVAEYIHENLGGKSVLEVMSTEGHLPHLSAPEITIPVLLRHINNDIVDA

Source

organism	Orobanche cernua var. cumana
ncbi_taxonomy_id	78542
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	pyrrolidine-1-carboxylic acid
formula_weight	115.1 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	218

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6. Citations (1)

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length_a	78.351 Å
length_b	78.351 Å
length_c	91.639 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32 2 1
int_tables_number	154
crystal_system	—

resolution	1.400 Å
resolution_low	39.210 Å
r_factor	0.1472
r_work	0.1463
r_free	0.1753

fit	/app/data/saxs_computation/wg/9wgn/9wgn.fit
pddf	/app/data/pr_computation/wg/9wgn/9wgn.pr.out
profile	/app/data/saxs_computation/wg/9wgn/9wgn.dat

Crystal structure of Orobanche cumana OcKAI2d2 covalently bound to KOK1007

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