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9vp5

Glucose-6-phosphate dehydrogenase from Leishmania donovani

Method: X-RAY DIFFRACTION D_max: 115.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vp5
deposition_date	2025-07-02
last_revision	2025-11-05
title	Glucose-6-phosphate dehydrogenase from Leishmania donovani
keywords	Glucose-6-phosphate dehydrogenase, Rossmann fold, apo form, 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	35.90 Å
rg_electron	35.02 Å
i0	196946000.00
molecular_weight	113780.0 kDa
excluded_volume	142640 Å³
envelope_volume	192870 Å³
shell_volume	45572 Å³
envelope_diameter	123.5 Å
shell_rg	42.09 Å
envelope_rg	34.16 Å
shape_rg	35.03 Å
total_rg	35.53 Å
total_atoms	8029
n_residues	1053
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	115.8 Å
rg_real	35.80 Å
rg_real_error	0.72 Å
i0_real	1.9690e+08
i0_real_error	2.9220e+06
rg_reciprocal	35.86 Å
i0_reciprocal	197000000.0000
total_estimate	0.9069
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	44.8 Å
skewness	0.197
kurtosis	-0.535
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	23670000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.979

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Glucose-6-phosphate 1-dehydrogenase
formula_weight	66933.8 kDa
ec_number	1.1.1.49
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8393

MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSEEQSHADQDAYVADVDGILDVLRAQVLERKPDDIFQFISKSALSLQKDRGAESCDRINCKVKDEQKSRALTIIVFGASGDLAKKKTFPALFDLYCGGLLPPEVNIIGYARTKVDDVEKWKHETLMKYFSNLSERGCHAEDFLKHISYFCGAYDSVDDFKRLDAVIREKENAFKGPEKGGNRLFYLALPPSVFASVCESIHKGAMPQEVGGWVRVIIEKPFGRDTKSSAELSQALEPFFDESQLYRIDHYLGKEMVQNIITTRFANRIFSAVWNASNIACVQITFKETIGTEGRGGYFDSIGIIRDVMQNHLTQILALLAMEKPRSLDAECIRDEKVSVLKCIEPITKENCVLGQYTASADGSIPGYLEDVTVPEGSTCPTFAVMRLNINNDRWAGVPFILKAGKAVEQKYVAIRIQFRDEVHPYGEATQRNELVIRAQPSEAMYVKITTKVPGLSGDLRQTHQTELDLTYHTRYDVRLPDAYESLINDALLGNSTNFVRKDELDVAWRIFTPLLHQIDSGEIKPIPYQAGTRGPKEADEFIANNGFKHQKGYHWLPSNKL

Source

organism	Leishmania donovani
ncbi_taxonomy_id	5661
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

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

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	364

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6. Citations (1)

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length_a	191.327 Å
length_b	97.356 Å
length_c	70.346 Å
angle_alpha	90.00 °
angle_beta	93.83 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.400 Å
resolution_low	54.886 Å
r_factor	—
r_work	0.1967
r_free	0.2593

fit	/app/data/saxs_computation/vp/9vp5/9vp5.fit
pddf	/app/data/pr_computation/vp/9vp5/9vp5.pr.out
profile	/app/data/saxs_computation/vp/9vp5/9vp5.dat

Glucose-6-phosphate dehydrogenase from Leishmania donovani

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