7X7K | pdb_00007x7k

Ancestral L-Lys oxidase (AncLLysO-2) L-Arg binding form

• PDB DOI: https://doi.org/10.2210/pdb7X7K/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-03-09 Released: 2023-01-18 
• Deposition Author(s): Motoyama, T., Ishida, C., Hasebe, F., Ito, S., Nakano, S.
• Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.160 (DCC) 

Starting Model: experimental

Literature

Reaction Mechanism of Ancestral l-Lys alpha-Oxidase from Caulobacter Species Studied by Biochemical, Structural, and Computational Analysis

Motoyama, T., Yamamoto, Y., Ishida, C., Hasebe, F., Kawamura, Y., Shigeta, Y., Ito, S., Nakano, S.

(2022) ACS Omega 7: 44407-44419

• DOI: https://doi.org/10.1021/acsomega.2c06334

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 132.24 kDa 
• Atom Count: 10,684 
• Modeled Residue Count: 1,166 
• Deposited Residue Count: 1,186 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAD dependent enzyme	A, B	593	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	C [auth A], E [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
ARG (Subject of Investigation/LOI)	D [auth A], F [auth B]	ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.160 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.258	α = 90
b = 77.214	β = 104.334
c = 93.258	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Motoyama, T., Ishida, C., Hasebe, F., Ito, S., Nakano, S.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJPR20AB
Japan Society for the Promotion of Science (JSPS)	Japan	21K05395
Japan Society for the Promotion of Science (JSPS)	Japan	19J23697

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary