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), 0.205 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4MKZ

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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.205 (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

View more in-depth experimental data

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 is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.