7D5N | pdb_00007d5n

Crystal structure of inositol dehydrogenase homolog complexed with NADH and myo-inositol from Azotobacter vinelandii

PDB DOI: https://doi.org/10.2210/pdb7D5N/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: 1.80 Å
R-Value Free:
0.197 (Depositor), 0.201 (DCC)
R-Value Work:
0.179 (Depositor), 0.187 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of inositol dehydrogenase complexed with NADH and myo-inositol 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: 90.43 kDa
Atom Count: 6,345
Modeled Residue Count: 768
Deposited Residue Count: 802
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase	A, B	401	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C1DLC3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI Query on NAI Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]
INS (Subject of Investigation/LOI) Query on INS Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE C₆ H₁₂ O₆ CDAISMWEOUEBRE-GPIVLXJGSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.197 (Depositor), 0.201 (DCC)
R-Value Work: 0.179 (Depositor), 0.187 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.81	α = 90
b = 151.53	β = 90
c = 48.12	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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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

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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.