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9x6l

Crystal structure of Klebsiella oxytoca ribitol dehydrogenase

Method: X-RAY DIFFRACTION D_max: 93.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9x6l
deposition_date	2025-10-15
last_revision	2026-04-29
title	Crystal structure of Klebsiella oxytoca ribitol dehydrogenase
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	29.82 Å
rg_electron	28.53 Å
i0	165450000.00
molecular_weight	104210.0 kDa
excluded_volume	131680 Å³
envelope_volume	158120 Å³
shell_volume	43938 Å³
envelope_diameter	105.6 Å
shell_rg	37.43 Å
envelope_rg	29.04 Å
shape_rg	28.52 Å
total_rg	29.38 Å
total_atoms	7328
n_residues	987
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	93.9 Å
rg_real	29.68 Å
rg_real_error	0.55 Å
i0_real	1.6550e+08
i0_real_error	2.2360e+06
rg_reciprocal	29.74 Å
i0_reciprocal	165500000.0000
total_estimate	0.8940
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.2 Å
skewness	0.221
kurtosis	-0.369
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	47750000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.931

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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	7514

MGSSHHHHHHSSGLVPRGSHSMNHSVSSMNTSLAGKVAAVTGAASGIGLECAKTLLGAGAKVVLIDREGEKLNKIVAELGENAFALQVDLMQAEQVDNILAGIVNLAGGLDIFHANAGAYIGGPVAEGDPDVWDRVLHLNINAAFRCVRSVLPHLIAQKSGDIIFTSSIAGVVPVIWEPIYTASKFAVQAFVHTTRRQVSQHGVRVGAVLPGPVVTALLDDWPKAKMDEALANGSLMQPIEVAESVLFMVTRSKNVTVRDIVILPNSVDL

Source

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

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	8

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	186

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6. Citations (1)

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length_a	64.049 Å
length_b	102.658 Å
length_c	80.984 Å
angle_alpha	90.00 °
angle_beta	109.86 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.970 Å
resolution_low	42.600 Å
r_factor	0.1861
r_work	0.1842
r_free	0.2237

fit	/app/data/saxs_computation/x6/9x6l/9x6l.fit
pddf	/app/data/pr_computation/x6/9x6l/9x6l.pr.out
profile	/app/data/saxs_computation/x6/9x6l/9x6l.dat

Crystal structure of Klebsiella oxytoca ribitol dehydrogenase

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