3DJD

Crystal structure of the deglycating enzyme fructosamine oxidase from Aspergillus fumigatus (Amadoriase II)

PDB DOI: https://doi.org/10.2210/pdb3DJD/pdb

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

Deposited: 2008-06-23 Released: 2008-07-22
Deposition Author(s): Collard, F., Zhang, J., Nemet, I., Qanungo, K.R., Monnier, V.M., Yee, V.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.204
R-Value Work: 0.167
R-Value Observed: 0.169

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 the deglycating enzyme fructosamine oxidase (FAOX-II)

Collard, F., Zhang, J., Nemet, I., Qanungo, K.R., Monnier, V.M., Yee, V.C.

To be published.

Macromolecule Content

Total Structure Weight: 100.43 kDa
Atom Count: 7,626
Modelled Residue Count: 835
Deposited Residue Count: 876
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructosyl amine: oxygen oxidoreductase	A, B	438	Aspergillus fumigatus	Mutation(s): 0
UniProt
Find proteins for P78573 (Aspergillus fumigatus) Explore P78573 Go to UniProtKB: P78573
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P78573
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.204
R-Value Work: 0.167
R-Value Observed: 0.169
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.31	α = 90
b = 54.266	β = 95.92
c = 106.252	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-07-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-07-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance

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 R01GM133198.