4MIY | pdb_00004miy

Crystal Structure of myo-inositol dehydrogenase from Lactobacillus casei in complex with NAD and myo-inositol

PDB DOI: https://doi.org/10.2210/pdb4MIY/pdb

Classification: OXIDOREDUCTASE
Organism(s): Lacticaseibacillus casei BL23
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-09-02 Released: 2015-03-04
Deposition Author(s): Bertwistle, D., Sanders, D.A.R., Palmer, D.R.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free:
0.207 (Depositor), 0.208 (DCC)
R-Value Work:
0.186 (Depositor), 0.186 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4MIY

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of myo-inositol dehydrogenase from Lactobacillus casei in complex with NAD and myo-inositol

Bertwistle, D., Aamudalapalli, H., Sanders, D.A.R., Palmer, D.R.J.

To be published.

Macromolecule Content

Total Structure Weight: 153.63 kDa
Atom Count: 12,059
Modeled Residue Count: 1,356
Deposited Residue Count: 1,356
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase	A, B, C, D	339	Lacticaseibacillus casei BL23	Mutation(s): 0 Gene Names: idh, iolG, iolG1, LCABL_02210 EC: 1.1.1.18 (PDB Primary Data), 1.1.1.369 (UniProt)
UniProt
Find proteins for A0A0J9X1Y2 (Lacticaseibacillus casei (strain BL23)) Explore A0A0J9X1Y2 Go to UniProtKB: A0A0J9X1Y2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0J9X1Y2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain P [auth C] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain W [auth D] MOL2 format, chain P [auth C] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain W [auth D] mmCIF format, chain P [auth C] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B], P [auth C], W [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain W [auth D]
INS Query on INS Download:Ideal Coordinates CCD File SDF format, chain X [auth D] MOL2 format, chain X [auth D] mmCIF format, chain X [auth D]	X [auth D]	1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE C₆ H₁₂ O₆ CDAISMWEOUEBRE-GPIVLXJGSA-N		Interactions Focus chain X [auth D] Interactions & Density Focus chain X [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain BA [auth D] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain BA [auth D]	BA [auth D] I [auth A] J [auth A] N [auth B] O [auth B] BA [auth D], I [auth A], J [auth A], N [auth B], O [auth B], U [auth C], V [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain U [auth C] Focus chain V [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain AA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain AA [auth D]	AA [auth D] F [auth A] G [auth A] H [auth A] L [auth B] AA [auth D], F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], Q [auth C], R [auth C], S [auth C], T [auth C], Y [auth D], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.207 (Depositor), 0.208 (DCC)
R-Value Work: 0.186 (Depositor), 0.186 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.711	α = 90
b = 110.624	β = 90
c = 127.015	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
SCALA	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MxDC	data collection
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-03-04

Deposition Author(s):

Sanders, D.A.R.

Revision History (Full details and data files)

Version 1.0: 2015-03-04
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.