4MKZ | pdb_00004mkz

Crystal Structure of apo scyllo-inositol dehydrogenase from Lactobacillus casei at 77K

PDB DOI: https://doi.org/10.2210/pdb4MKZ/pdb

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

Deposited: 2013-09-06 Released: 2015-03-04
Deposition Author(s): Bertwistle, D., Linda, V., Sanders, D.A.R., Palmer, D.R.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.229 (Depositor), 0.230 (DCC)
R-Value Work:
0.204 (Depositor), 0.200 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of apo scyllo-inositol dehydrogenase from Lactobacillus casei at 77K

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

To be published.

Macromolecule Content

Total Structure Weight: 39.27 kDa
Atom Count: 2,831
Modeled Residue Count: 336
Deposited Residue Count: 355
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol dehydrogenase	A	355	Lacticaseibacillus casei BL23	Mutation(s): 0 Gene Names: idh, iolG, iolG2, LCABL_02220 EC: 1.1.1
UniProt
Find proteins for A5YBJ8 (Lacticaseibacillus casei) Explore A5YBJ8 Go to UniProtKB: A5YBJ8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5YBJ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.229 (Depositor), 0.230 (DCC)
R-Value Work: 0.204 (Depositor), 0.200 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.45	α = 90
b = 121.65	β = 90
c = 130.94	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MxDC	data collection

Structure Validation

View Full Validation Report

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

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.