SAXSdb — 9x6n

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	ISOPROPYL ALCOHOL × 4 alpha-D-psicopyranose × 1 D-psicose × 1 alpha-D-psicofuranose × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

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	9x6n
Deposition date deposition_date	2025-10-15
Last revision last_revision	2026-04-29
Structure title title	Crystal structure of Klebsiella oxytoca ribitol dehydrogenase in complex with D-allulose
Keywords keywords	Rossmann fold, dehydrogenase, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9x6n__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9x6n__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9x6n__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	30.13 Å
Rg (electron density)	28.79 Å
Total Rg	29.63 Å
Atom count	7445
Residues	1005
Excluded volume	133480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9x6n__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

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	7928

MGSSHHHHHHSSGLVPRGSHSMNHSVSSMNTSLAGKVAAVTGAASGIGLECAKTLLGAGAKVVLIDREGEKLNKIVAELGENAFALQVDLMQAEQVDNILAGIVNLAGGLDIFHANAGAYIGGPVAEGDPDVWDRVLHLNINAAFRCVRSVLPHLIAQKSGDIIFTSSIAGVVPVIWEPIYTASKFAVQAFVHTTRRQVSQHGVRVGAVLPGPVVTALLDDWPKAKMDEALANGSLMQPIEVAESVLFMVTRSKNVTVRDIVILPNSVDL

Source Source

Source organism organism	Klebsiella oxytoca
NCBI taxonomy ID ncbi_taxonomy_id	571
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	alpha-D-psicopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	D-psicose
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	alpha-D-psicofuranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	454

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Unit-cell length a length_a	64.008 Å
Unit-cell length b length_b	102.869 Å
Unit-cell length c length_c	80.574 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.70 °
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	1.560 Å
Low-resolution limit resolution_low	42.610 Å
R factor r_factor	0.1698
R_work r_work	0.1687
R_free r_free	0.1923

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9x6n__assembly_1__model_1

9x6n__assembly_1__model_1 | I(q)

9x6n__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

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

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9x6n__assembly_1__model_1

9x6n__assembly_1__model_1 | I(q)

9x6n__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)