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9vp6

Glucose-6-phosphate dehydrogenase from Leishmania donovani in complex with substrate

Method: X-RAY DIFFRACTION D_max: 117.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vp6
deposition_date	2025-07-02
last_revision	2025-11-05
title	Glucose-6-phosphate dehydrogenase from Leishmania donovani in complex with substrate
keywords	Glucose-6-phosphate dehydrogenase, Rossmann fold, complex form, substrate, 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	35.77 Å
rg_electron	34.96 Å
i0	204610000.00
molecular_weight	116160.0 kDa
excluded_volume	145840 Å³
envelope_volume	196360 Å³
shell_volume	46479 Å³
envelope_diameter	123.5 Å
shell_rg	41.98 Å
envelope_rg	34.22 Å
shape_rg	34.97 Å
total_rg	35.46 Å
total_atoms	8188
n_residues	1059
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	117.6 Å
rg_real	35.69 Å
rg_real_error	0.91 Å
i0_real	2.0460e+08
i0_real_error	3.4190e+06
rg_reciprocal	35.74 Å
i0_reciprocal	204600000.0000
total_estimate	0.9016
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	45.4 Å
skewness	0.217
kurtosis	-0.517
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	25740000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.979

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

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	8761

MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSEEQSHADQDAYVADVDGILDVLRAQVLERKPDDIFQFISKSALSLQKDRGAESCDRINCKVKDEQKSRALTIIVFGASGDLAKKKTFPALFDLYCGGLLPPEVNIIGYARTKVDDVEKWKHETLMKYFSNLSERGCHAEDFLKHISYFCGAYDSVDDFKRLDAVIREKENAFKGPEKGGNRLFYLALPPSVFASVCESIHKGAMPQEVGGWVRVIIEKPFGRDTKSSAELSQALEPFFDESQLYRIDHYLGKEMVQNIITTRFANRIFSAVWNASNIACVQITFKETIGTEGRGGYFDSIGIIRDVMQNHLTQILALLAMEKPRSLDAECIRDEKVSVLKCIEPITKENCVLGQYTASADGSIPGYLEDVTVPEGSTCPTFAVMRLNINNDRWAGVPFILKAGKAVEQKYVAIRIQFRDEVHPYGEATQRNELVIRAQPSEAMYVKITTKVPGLSGDLRQTHQTELDLTYHTRYDVRLPDAYESLINDALLGNSTNFVRKDELDVAWRIFTPLLHQIDSGEIKPIPYQAGTRGPKEADEFIANNGFKHQKGYHWLPSNKL

Source

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

Entity 2 non-polymer

description	6-O-phosphono-beta-D-glucopyranose
formula_weight	260.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	573

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6. Citations (1)

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length_a	193.396 Å
length_b	92.381 Å
length_c	70.628 Å
angle_alpha	90.00 °
angle_beta	94.44 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.300 Å
resolution_low	29.554 Å
r_factor	—
r_work	0.2278
r_free	0.3142

fit	/app/data/saxs_computation/vp/9vp6/9vp6.fit
pddf	/app/data/pr_computation/vp/9vp6/9vp6.pr.out
profile	/app/data/saxs_computation/vp/9vp6/9vp6.dat