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9x6n

Crystal structure of Klebsiella oxytoca ribitol dehydrogenase in complex with D-allulose

Method: X-RAY DIFFRACTION D_max: 94.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9x6n
deposition_date	2025-10-15
last_revision	2026-04-29
title	Crystal structure of Klebsiella oxytoca ribitol dehydrogenase in complex with D-allulose
keywords	Rossmann fold, 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	30.13 Å
rg_electron	28.79 Å
i0	172819000.00
molecular_weight	105890.0 kDa
excluded_volume	133480 Å³
envelope_volume	161730 Å³
shell_volume	44634 Å³
envelope_diameter	105.6 Å
shell_rg	37.66 Å
envelope_rg	29.23 Å
shape_rg	28.78 Å
total_rg	29.63 Å
total_atoms	7445
n_residues	1005
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	94.4 Å
rg_real	29.99 Å
rg_real_error	0.52 Å
i0_real	1.7280e+08
i0_real_error	2.3540e+06
rg_reciprocal	30.05 Å
i0_reciprocal	172800000.0000
total_estimate	0.8970
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.4 Å
skewness	0.230
kurtosis	-0.365
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	45480000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.955

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Ribitol 2-dehydrogenase
formula_weight	28532.7 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	7928

MGSSHHHHHHSSGLVPRGSHSMNHSVSSMNTSLAGKVAAVTGAASGIGLECAKTLLGAGAKVVLIDREGEKLNKIVAELGENAFALQVDLMQAEQVDNILAGIVNLAGGLDIFHANAGAYIGGPVAEGDPDVWDRVLHLNINAAFRCVRSVLPHLIAQKSGDIIFTSSIAGVVPVIWEPIYTASKFAVQAFVHTTRRQVSQHGVRVGAVLPGPVVTALLDDWPKAKMDEALANGSLMQPIEVAESVLFMVTRSKNVTVRDIVILPNSVDL

Source

organism	Klebsiella oxytoca
ncbi_taxonomy_id	571
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ISOPROPYL ALCOHOL
formula_weight	60.1 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	alpha-D-psicopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	D-psicose
formula_weight	180.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	alpha-D-psicofuranose
formula_weight	180.2 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	454

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6. Citations (1)

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length_a	64.008 Å
length_b	102.869 Å
length_c	80.574 Å
angle_alpha	90.00 °
angle_beta	109.70 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.560 Å
resolution_low	42.610 Å
r_factor	0.1698
r_work	0.1687
r_free	0.1923

fit	/app/data/saxs_computation/x6/9x6n/9x6n.fit
pddf	/app/data/pr_computation/x6/9x6n/9x6n.pr.out
profile	/app/data/saxs_computation/x6/9x6n/9x6n.dat