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9vpz

Crystal structure of wild-type Trypanosoma brucei DHODH in FMN-reduced, ligand-free form

Method: X-RAY DIFFRACTION D_max: 109.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vpz
deposition_date	2025-07-04
title	Crystal structure of wild-type Trypanosoma brucei DHODH in FMN-reduced, ligand-free form
keywords	Ping-Pong Reaction Mechanism, Substrate/Product-enzyme interactions., FLAVOPROTEIN; FLAVOPROTEIN
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	34.54 Å
rg_electron	34.08 Å
i0	291173000.00
molecular_weight	139560.0 kDa
excluded_volume	175210 Å³
envelope_volume	201850 Å³
shell_volume	48184 Å³
envelope_diameter	112.1 Å
shell_rg	41.44 Å
envelope_rg	33.94 Å
shape_rg	34.07 Å
total_rg	34.58 Å
total_atoms	9781
n_residues	1248
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	109.8 Å
rg_real	34.46 Å
rg_real_error	0.79 Å
i0_real	2.9120e+08
i0_real_error	4.9780e+06
rg_reciprocal	34.51 Å
i0_reciprocal	291200000.0000
total_estimate	0.9038
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	38.2 Å
skewness	0.203
kurtosis	-0.617
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	105400000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.920

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Dihydroorotate dehydrogenase (fumarate)
formula_weight	34473.7 kDa
ec_number	1.3.98.1
mutation	A115V
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,C,B,D
atom_count	10213

GPGSMSLKVNILGHEFSNPFMNAAGVLCTTEEDLRRMTESESGSLIGKSCTLAPRTGNPEPRYFGLPLGSINSMGLPNLGVDFYLSYAAQTHDYSRKPLFLSMSGLSVEESVEMVKKLVPITKEKGTILELNLSCPNVPGKPQVGYDFDTTRTYLQKVSEAYGLPFGVKMPPYFDIAHFDMAAAVLNDFPLVKFITCVNSIGNGLVIDPANETVVIKPKQGFGGLGGKYVLPTALANVNAFFRRCPDKLVFGCGGVYSGEEAFLHILAGASMVQVGTALHDEGPIIFARLNKELQEIMTNKGYKTLDEFRGRVKTMD

Source

organism	Trypanosoma brucei brucei TREU927
ncbi_taxonomy_id	185431
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL
formula_weight	458.4 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	MALONATE ION
formula_weight	102.0 kDa
src_method	nat
entity_count	11

Entity 4 non-polymer

description	SULFUR DIOXIDE
formula_weight	64.1 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	SULFITE ION
formula_weight	80.1 kDa
src_method	syn
entity_count	4

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	432

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6. Citations (1)

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length_a	139.376 Å
length_b	146.632 Å
length_c	65.594 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	1.750 Å
resolution_low	48.880 Å
r_factor	0.1827
r_work	0.1816
r_free	0.2024

fit	/app/data/saxs_computation/vp/9vpz/9vpz.fit
pddf	/app/data/pr_computation/vp/9vpz/9vpz.pr.out
profile	/app/data/saxs_computation/vp/9vpz/9vpz.dat