SAXSdb — 3cea

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

Myo-inositol 2-dehydrogenase

Lactobacillus plantarum WCFS1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 CHLORIDE ION × 1 1,2-ETHANEDIOL × 3 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q88S39_LACPL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–346； UniProt 1–345 Author chain B； PDBConstruct 2–346； UniProt 1–345 Author chain C； PDBConstruct 2–346； UniProt 1–345 Author chain D； PDBConstruct 2–346； UniProt 1–345

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	3cea
Deposition date deposition_date	2008-02-28
Structure title title	Crystal structure of myo-inositol 2-dehydrogenase (NP_786804.1) from Lactobacillus plantarum at 2.40 A resolution
Keywords keywords	;NP_786804.1, myo-inositol 2-dehydrogenase, Oxidoreductase family, NAD-binding Rossmann fold, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, 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.

3cea__assembly_1__model_1

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

Download this curve (.dat)

3cea__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cea__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.42 Å
Rg (electron density)	34.95 Å
Total Rg	35.49 Å
Atom count	10624
Residues	1322
Excluded volume	188490 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cea__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 (5)

Entity 1 Entity 1 polymer

Description description	Myo-inositol 2-dehydrogenase
Molecular weight formula_weight	38713.1 kDa
EC 编号 ec_number	1.1.1.18
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	10991

GMVTTRKPLRAAIIGLGRLGERHARHLVNKIQGVKLVAACALDSNQLEWAKNELGVETTYTNYKDMIDTENIDAIFIVAPTPFHPEMTIYAMNAGLNVFCEKPLGLDFNEVDEMAKVIKSHPNQIFQSGFMRRYDDSYRYAKKIVDNGDIGKIIYMRGYGIDPISGMESFTKFATEADSGGIFVDMNIHDIDLIRWFTGQDPVQAYGLTSNIAAPQLADIGEFETGVAQLKMSDGVIATLIGGRHAAHGNQVELEVMGSNGWVRIGEHPDLNRVTVFNDQGVVRPSLQSFGERFDTAFTDEVQDFVNNVIVGKQPEVTVDDGIKALKIAKACQQSANIGKLVDIQL

Source Source

Source organism organism	Lactobacillus plantarum WCFS1
NCBI taxonomy ID ncbi_taxonomy_id	220668
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	343

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	3ceaA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3ceaA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	3ceaB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3ceaB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	3ceaC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3ceaC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	3ceaD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3ceaD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

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Unit-cell length a length_a	47.331 Å
Unit-cell length b length_b	145.684 Å
Unit-cell length c length_c	100.208 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.92 °
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	2.400 Å
Low-resolution limit resolution_low	29.450 Å
R factor r_factor	0.1960
R_work r_work	0.1930
R_free r_free	0.2430

Crystal structure of myo-inositol 2-dehydrogenase (NP_786804.1) from Lactobacillus plantarum at 2.40 A resolution

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

Myo-inositol 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

3cea__assembly_1__model_1

3cea__assembly_1__model_1 | I(q)

3cea__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of myo-inositol 2-dehydrogenase (NP_786804.1) from Lactobacillus plantarum at 2.40 A resolution

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

Myo-inositol 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

3cea__assembly_1__model_1

3cea__assembly_1__model_1 | I(q)

3cea__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)