SAXSdb — 9x6m

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ribitol 2-dehydrogenase

Klebsiella oxytoca

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–249 Chain B； UniProt 1–249 Chain C； UniProt 1–249 Chain D； UniProt 1–249	Not recorded	ALL beta-D-allopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；lithium sulfate, PEG3350, Tris	Resolution 1.73 Å R-free 0.192

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9X6M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9X6L Crystal structure of Klebsiella oxytoca ribitol dehydrogenase Deposited 2025-10-15	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–249（249 aa） Chain B 1–249（249 aa） Chain C 1–249（249 aa） Chain D 1–249（249 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；lithium sulfate, PEG3350, Tris	Resolution 1.97 Å R-free 0.224
9X6N Crystal structure of Klebsiella oxytoca ribitol dehydrogenase in complex with D-allulose Deposited 2025-10-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–249（249 aa） Chain B 1–249（249 aa） Chain C 1–249（249 aa） Chain D 1–249（249 aa）	Not recorded	IPA ISOPROPYL ALCOHOL × 4 WEB alpha-D-psicopyranose × 1 PSJ D-psicose × 1 PSV alpha-D-psicofuranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；ammonium sulfate, isopropanol, PEG8000, HEPES	Resolution 1.56 Å R-free 0.192
9X6O Crystal structure of Klebsiella oxytoca ribitol dehydrogenase in complex with NAD+ Deposited 2025-10-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–249（249 aa） Chain B 1–249（249 aa） Chain C 1–249（249 aa） Chain D 1–249（249 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；calcium acetate, PEG400, acetate, NAD+	Resolution 1.89 Å R-free 0.220

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A318FHD8_KLEOX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–270； UniProt 1–249 Author chain B； PDBConstruct 22–270； UniProt 1–249 Author chain C； PDBConstruct 22–270； UniProt 1–249 Author chain D； PDBConstruct 22–270； UniProt 1–249

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9x6m
Deposition date deposition_date	2025-10-15
最后修订 last_revision	2026-04-29
Structure title title	Crystal structure of Klebsiella oxytoca ribitol dehydrogenase in complex with D-allose
Keywords keywords	Rossmann fold, dehydrogenase, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	29.67 Å
Radius of gyration Rg (electron density) rg_electron	28.46 Å
Forward intensity I(0) i0	157224000.00
Molecular weight molecular_weight	101710.0 kDa
Excluded volume excluded_volume	128500 Å³
Envelope volume envelope_volume	152860 Å³
Hydration-shell volume shell_volume	42841 Å³
Envelope diameter envelope_diameter	108.9 Å
Shell Rg shell_rg	37.18 Å
Envelope Rg envelope_rg	29.03 Å
Shape Rg shape_rg	28.45 Å
Total Rg total_rg	29.28 Å
Total atoms total_atoms	14491
Residues n_residues	967
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	100.6 Å
Rg (real space) rg_real	29.56 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	1.5720e+08
I(0) uncertainty (real space) i0_real_error	2.3350e+06
Rg (reciprocal space) rg_reciprocal	29.61 Å
I(0) (reciprocal space) i0_reciprocal	157200000.0000
Solution quality estimate total_estimate	0.6567
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.0 Å
Skewness Skewness skewness	0.259
Kurtosis Kurtosis kurtosis	-0.326
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	49620000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.794; Stabil: 1.000; Sysdev: 0.050; Positv: 1.000; Valcen: 1.000; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Ribitol 2-dehydrogenase
Molecular weight formula_weight	28532.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	15184

MGSSHHHHHHSSGLVPRGSHSMNHSVSSMNTSLAGKVAAVTGAASGIGLECAKTLLGAGAKVVLIDREGEKLNKIVAELGENAFALQVDLMQAEQVDNILAGIVNLAGGLDIFHANAGAYIGGPVAEGDPDVWDRVLHLNINAAFRCVRSVLPHLIAQKSGDIIFTSSIAGVVPVIWEPIYTASKFAVQAFVHTTRRQVSQHGVRVGAVLPGPVVTALLDDWPKAKMDEALANGSLMQPIEVAESVLFMVTRSKNVTVRDIVILPNSVDL

来源 Source

来源生物 organism	Klebsiella oxytoca
NCBI Class编号 ncbi_taxonomy_id	571
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	beta-D-allopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	669

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8. Citations (1)

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Unit-cell length a length_a	64.184 Å
Unit-cell length b length_b	102.899 Å
Unit-cell length c length_c	81.488 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.14 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.730 Å
Low-resolution limit resolution_low	40.972 Å
R factor r_factor	0.1612
R_work r_work	0.1596
R_free r_free	0.1921

fit	/app/data/saxs_computation/x6/9x6m/9x6m.fit
pddf	/app/data/pr_computation/x6/9x6m/9x6m.pr.out
profile	/app/data/saxs_computation/x6/9x6m/9x6m.dat

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ribitol 2-dehydrogenase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction