7VKD | pdb_00007vkd

Reduced enzyme of FAD-dpendent Glucose Dehydrogenase at pH6.5

PDB DOI: https://doi.org/10.2210/pdb7VKD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aspergillus oryzae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-09-29 Released: 2022-10-05
Deposition Author(s): Nakajima, Y., Nishiya, Y., Ito, K.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free:
0.183 (Depositor), 0.180 (DCC)
R-Value Work:
0.150 (Depositor), 0.150 (DCC)
R-Value Observed:
0.152 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Conformational change of catalytic residue in reduced enzyme of FAD-dependent Glucose Dehydrogenase at pH6.5

Nakajima, Y.

To be published.

Macromolecule Content

Total Structure Weight: 62.47 kDa
Atom Count: 4,998
Modeled Residue Count: 563
Deposited Residue Count: 572
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GMC oxidoreductase	A	572	Aspergillus oryzae	Mutation(s): 0 Gene Names: OAory_01010120 EC: 1.1.3.4
UniProt
Find proteins for A0A1S9DW10 (Aspergillus oryzae) Explore A0A1S9DW10 Go to UniProtKB: A0A1S9DW10
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1S9DW10
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FDA (Subject of Investigation/LOI) Query on FDA 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]	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE C₂₇ H₃₅ N₉ O₁₅ P₂ YPZRHBJKEMOYQH-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free: 0.183 (Depositor), 0.180 (DCC)
R-Value Work: 0.150 (Depositor), 0.150 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.09	α = 90
b = 94.09	β = 90
c = 123.867	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-10-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	24780106

Revision History (Full details and data files)

Version 1.0: 2022-10-05
Type: Initial release
Version 1.1: 2022-10-12
Changes: Structure summary
Version 1.2: 2024-05-29
Changes: Data collection

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.