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9x6o

Crystal structure of Klebsiella oxytoca ribitol dehydrogenase in complex with NAD+

Method: X-RAY DIFFRACTION Dmax: 90.6 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ribitol 2-dehydrogenase

Klebsiella oxytoca

UniProt A0A318FHD8

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 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

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 9X6O 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 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 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
9X6M Crystal structure of Klebsiella oxytoca ribitol dehydrogenase in complex with D-allose 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 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
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

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 1–249； UniProt 1–249 Author chain B； PDBConstruct 1–249； UniProt 1–249 Author chain C； PDBConstruct 1–249； UniProt 1–249 Author chain D； PDBConstruct 1–249； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 9x6o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9x6o
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9x6o
Deposition date deposition_date2025-10-15
最后修订 last_revision2026-04-29
Structure title titleCrystal structure of Klebsiella oxytoca ribitol dehydrogenase in complex with NAD+
Keywords keywordsRossmann fold, dehydrogenase, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.22 Å
Radius of gyration Rg (electron density) rg_electron27.99 Å
Forward intensity I(0) i0168071000.00
Molecular weight molecular_weight104040.0 kDa
Excluded volume excluded_volume130880 ų
Envelope volume envelope_volume151840 ų
Hydration-shell volume shell_volume43120 ų
Envelope diameter envelope_diameter95.2 Å
Shell Rg shell_rg36.92 Å
Envelope Rg envelope_rg28.09 Å
Shape Rg shape_rg27.98 Å
Total Rg total_rg28.83 Å
Total atoms total_atoms7311
Residues n_residues965
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax90.6 Å
Rg (real space) rg_real29.06 Å
Rg uncertainty (real space) rg_real_error0.46 Å
I(0) (real space) i0_real1.6810e+08
I(0) uncertainty (real space) i0_real_error2.5310e+06
Rg (reciprocal space) rg_reciprocal29.13 Å
I(0) (reciprocal space) i0_reciprocal168100000.0000
Solution quality estimate total_estimate0.9002
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.9 Å
Skewness Skewness skewness0.144
Kurtosis Kurtosis kurtosis-0.469
Angular range angular_range— – 0.2700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha66760000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.966
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)