3CEA | pdb_00003cea

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

PDB DOI: https://doi.org/10.2210/pdb3CEA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Lactiplantibacillus plantarum WCFS1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-02-28 Released: 2008-03-11
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.243 (Depositor), 0.244 (DCC)
R-Value Work:
0.193 (Depositor), 0.197 (DCC)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

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

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 157.73 kDa
Atom Count: 10,991
Modeled Residue Count: 1,362
Deposited Residue Count: 1,384
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myo-inositol 2-dehydrogenase	A, B, C, D	346	Lactiplantibacillus plantarum WCFS1	Mutation(s): 0 Gene Names: NP_786804.1, iolG1, lp_3605 EC: 1.1.1.18 (PDB Primary Data), 1.1.1 (UniProt)
UniProt
Find proteins for F9ULF9 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore F9ULF9 Go to UniProtKB: F9ULF9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F9ULF9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain J [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain J [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth C] mmCIF format, chain J [auth D]	E [auth A], G [auth B], H [auth C], J [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain J [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain K [auth D] SDF format, chain L [auth D] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D]	I [auth C], K [auth D], L [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain I [auth C] Focus chain K [auth D] Focus chain L [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.243 (Depositor), 0.244 (DCC)
R-Value Work: 0.193 (Depositor), 0.197 (DCC)
R-Value Observed: 0.196 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.331	α = 90
b = 145.684	β = 91.92
c = 100.208	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
SHARP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-03-11

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-03-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Data collection, Refinement description, Structure summary