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9zo1

Crystal structure of deoxypodophyllotoxin synthase (DPS) complexed with vanadyl(IV)-oxo, succinate and (-)-hydroxy-yatein

Method: X-RAY DIFFRACTION D_max: 108.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zo1
deposition_date	2025-12-15
last_revision	2026-06-03
title	Crystal structure of deoxypodophyllotoxin synthase (DPS) complexed with vanadyl(IV)-oxo, succinate and (-)-hydroxy-yatein
keywords	Oxygenase, Fe/2OG, OXIDOREDUCTASE; OXIDOREDUCTASE
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	30.07 Å
rg_electron	29.65 Å
i0	163571000.00
molecular_weight	67988.0 kDa
excluded_volume	65716 Å³
envelope_volume	112450 Å³
shell_volume	32427 Å³
envelope_diameter	117.1 Å
shell_rg	35.88 Å
envelope_rg	29.69 Å
shape_rg	29.66 Å
total_rg	30.06 Å
total_atoms	5126
n_residues	628
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	108.6 Å
rg_real	30.21 Å
rg_real_error	0.96 Å
i0_real	1.6360e+08
i0_real_error	2.4440e+06
rg_reciprocal	30.15 Å
i0_reciprocal	163600000.0000
total_estimate	0.8283
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.7 Å
skewness	0.457
kurtosis	-0.365
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	28880000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.669; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.797; Smooth: 0.959

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Deoxypodophyllotoxin synthase
formula_weight	36140.1 kDa
ec_number	1.14.20.8
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5811

MGSTAPLRLPVIDLSMKNLKPGTTSWNSVRTQVREALEEYGCFEAVIDAVSPELQKAVCNKGHELLNLPLETKMLNGNKPEYDGFTSIPNLNEGMGVGRITDLEKVERFTNLMWPEGNKDFCETVYSYGKRMAEVDHILKMMVFESFGMEKHFDSFCESTNYLLHFMRYQQPGKDGRSPALSLHKDKSILTIVNQNDVKGLEFETKDGEWILPTADNHIVLLGDCFMAWSNGRLHSPLHRVTLVANQARLSTSSFSFPKDIIETPAELVDEEHPLLFNPFEITELLAYCFTKEGAKAVCDLKQYKAYTGALEHHHHHH

Source

organism	Sinopodophyllum hexandrum
ncbi_taxonomy_id	93608
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	oxovanadium(2+)
formula_weight	66.9 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	(3S,4S)-4-[(S)-(2H-1,3-benzodioxol-5-yl)(hydroxy)methyl]-3-[(3,4,5-trimethoxyphenyl)methyl]oxolan-2-one
formula_weight	416.4 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	SUCCINIC ACID
formula_weight	118.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

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

Entity 6 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 7 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	nat
entity_count	2

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	638

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6. Citations (1)

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length_a	78.927 Å
length_b	87.635 Å
length_c	100.249 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	orthorhombic

resolution	2.000 Å
resolution_low	17.990 Å
r_factor	0.1641
r_work	0.1614
r_free	0.2117

fit	/app/data/saxs_computation/zo/9zo1/9zo1.fit
pddf	/app/data/pr_computation/zo/9zo1/9zo1.pr.out
profile	/app/data/saxs_computation/zo/9zo1/9zo1.dat