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10gw

Crystal structure of tetrameric 6-phosphogluconate dehydrogenase from Gluconobacter oxydans in complex with 6-phosphogluconate

Method: X-RAY DIFFRACTION D_max: 117.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	10gw
deposition_date	2026-01-19
last_revision	2026-03-18
title	Crystal structure of tetrameric 6-phosphogluconate dehydrogenase from Gluconobacter oxydans in complex with 6-phosphogluconate
keywords	Oxidative pentose phosphate pathway, 6-phosphogluconate dehydrogenase, dehydrogenase, 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	35.30 Å
rg_electron	34.64 Å
i0	350709000.00
molecular_weight	144900.0 kDa
excluded_volume	178460 Å³
envelope_volume	218690 Å³
shell_volume	51979 Å³
envelope_diameter	120.0 Å
shell_rg	41.61 Å
envelope_rg	34.93 Å
shape_rg	34.63 Å
total_rg	35.09 Å
total_atoms	19986
n_residues	1332
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	117.8 Å
rg_real	35.24 Å
rg_real_error	0.87 Å
i0_real	3.5070e+08
i0_real_error	5.5960e+06
rg_reciprocal	35.28 Å
i0_reciprocal	350700000.0000
total_estimate	0.7003
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	44.5 Å
skewness	0.283
kurtosis	-0.403
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	113400000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 0.186; Positv: 1.000; Valcen: 0.999; Smooth: 0.936

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	6-phosphogluconate dehydrogenase
formula_weight	38332.0 kDa
ec_number	1.1.1.343
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	20362

MGSSHHHHHHSSGENLYFQGHMRIGIIGLGRMGGNIAVRLTRHGHDVVVHDRTSEVTTSVVGRCEAGRATPADTLADMAKLLEGDEHRVVWVMLPAGAITEDCVQQLGGLLGRGDIIIDGGNTYYKDDVRRSAELAEKGISYVDVGTSGGVWGLERGYCMMFGGTKETAEYIDPILSALAPGIGDVPRTPGRDEAGHDPRAEQGYLHCGPAGSGHFVKMVHNGIEYGMMQAFAEGFDIMKSKNSPILAEKDRFELNMGDIAEVWRRGSVVSSWLLDLTAEALTRSETLNEFSGEVADSGEGRWTIEAAIEEDVPAPVMTAALFTRFRSRSGNNFAEKILSAQRFGFGGHVEKK

Source

organism	Gluconobacter oxydans
ncbi_taxonomy_id	442
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	6-PHOSPHOGLUCONIC ACID
formula_weight	276.1 kDa
src_method	syn
entity_count	4

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	376

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6. Citations (2)

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length_a	54.118 Å
length_b	79.241 Å
length_c	86.533 Å
angle_alpha	102.17 °
angle_beta	97.00 °
angle_gamma	99.40 °
z_pdb	4

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	2.000 Å
resolution_low	41.610 Å
r_factor	0.1951
r_work	0.1935
r_free	0.2244

fit	/app/data/saxs_computation/0g/10gw/10gw.fit
pddf	/app/data/pr_computation/0g/10gw/10gw.pr.out
profile	/app/data/saxs_computation/0g/10gw/10gw.dat

Crystal structure of tetrameric 6-phosphogluconate dehydrogenase from Gluconobacter oxydans in complex with 6-phosphogluconate

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