7X7I | pdb_00007x7i

Ancestral L-Lys oxidase (AncLLysO-2) ligand free form

PDB DOI: https://doi.org/10.2210/pdb7X7I/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.191 (Depositor), 0.198 (DCC)
R-Value Work:
0.163 (Depositor)

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Ligand Structure Quality Assessment

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

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

Macromolecule Content

Total Structure Weight: 131.89 kDa
Atom Count: 10,495
Modeled Residue Count: 1,166
Deposited Residue Count: 1,186
Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD 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]	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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.191 (Depositor), 0.198 (DCC)
R-Value Work: 0.163 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.246	α = 90
b = 76.533	β = 104.389
c = 92.708	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-18

Deposition Author(s):

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 (Full details and data files)

Version 1.0: 2023-01-18
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Structure summary

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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.