7C4M | pdb_00007c4m

Ancestral L-amino acid oxidase (AncLAAO-N5) L-Trp binding form

PDB DOI: https://doi.org/10.2210/pdb7C4M/pdb

Classification: OXIDOREDUCTASE
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2020-05-18 Released: 2020-12-02
Deposition Author(s): Nakano, S., Minamino, Y., Karasuda, H., Ito, S.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.270 (Depositor), 0.270 (DCC)
R-Value Work:
0.208 (Depositor), 0.210 (DCC)
R-Value Observed:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids

Nakano, S., Kozuka, K., Minamino, Y., Karasuda, H., Hasebe, F., Ito, S.

(2020) Commun Chem 3

DOI: https://doi.org/10.1038/s42004-020-00432-8

Macromolecule Content

Total Structure Weight: 75.95 kDa
Atom Count: 5,181
Modeled Residue Count: 614
Deposited Residue Count: 663
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ancestral L-amino acid oxidase	A	663	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
TRP Query on TRP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	TRYPTOPHAN C₁₁ H₁₂ N₂ O₂ QIVBCDIJIAJPQS-VIFPVBQESA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.270 (Depositor), 0.270 (DCC)
R-Value Work: 0.208 (Depositor), 0.210 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.499	α = 90
b = 132.499	β = 90
c = 191.732	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	refinement
SCALA	data scaling
AutoSol	phasing
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-12-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	16K18688
Japan Society for the Promotion of Science (JSPS)	Japan	18K14391

Revision History (Full details and data files)

Version 1.0: 2020-12-02
Type: Initial release
Version 1.1: 2021-01-06
Changes: Database references
Version 1.2: 2024-03-27
Changes: Data collection, Database references

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.