7D5M | pdb_00007d5m

Crystal structure of inositol dehydrogenase homolog complexed with NAD+ from Azotobacter vinelandii

PDB DOI: https://doi.org/10.2210/pdb7D5M/pdb

Classification: OXIDOREDUCTASE
Organism(s): Azotobacter vinelandii DJ
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-09-27 Released: 2021-09-29
Deposition Author(s): Fukano, K., Ono, T., Suzuki, M., Takenoya, M., Ito, S., Sasaki, Y., Yajima, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.193 (Depositor), 0.200 (DCC)
R-Value Work:
0.179 (Depositor), 0.190 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of inositol dehydrogenase complexed with NAD+ from Azotobacter vinelandii

Fukano, K., Ono, T., Suzuki, M., Takenoya, M., Ito, S., Sasaki, Y., Yajima, S.

To be published.

Macromolecule Content

Total Structure Weight: 44.8 kDa
Atom Count: 3,344
Modeled Residue Count: 389
Deposited Residue Count: 397
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase	A	397	Azotobacter vinelandii DJ	Mutation(s): 0 Gene Names: Avin_50260
UniProt
Find proteins for C1DLC3 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore C1DLC3 Go to UniProtKB: C1DLC3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C1DLC3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD 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]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.193 (Depositor), 0.200 (DCC)
R-Value Work: 0.179 (Depositor), 0.190 (DCC)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.25	α = 90
b = 107.997	β = 90
c = 156.759	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-09-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-09-29
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Derived calculations, Refinement description

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.