5OXT

DIRECT-EVOLUTIONED UNSPECIFIC PEROXYGENASE FROM AGROCYBE AEGERITA, IN COMPLEX WITH ACETATE

PDB DOI: https://doi.org/10.2210/pdb5OXT/pdb

Classification: OXIDOREDUCTASE
Organism(s): Cyclocybe aegerita
Expression System: Komagataella phaffii CBS 7435
Mutation(s): Yes

Deposited: 2017-09-07 Released: 2019-04-17
Deposition Author(s): Ramirez-Escudero, M., Sanz-Aparicio, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.164
R-Value Work: 0.150
R-Value Observed: 0.151

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 113.16 kDa
Atom Count: 9,345
Modelled Residue Count: 981
Deposited Residue Count: 984
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UNSPECIFIC PEROXYGENASE	A, B, C	328	Cyclocybe aegerita	Mutation(s): 5 Gene Names: APO1 EC: 1.11.2.1
UniProt
Find proteins for B9W4V6 (Cyclocybe aegerita) Explore B9W4V6 Go to UniProtKB: B9W4V6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B9W4V6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain D [auth A] SDF format, chain X [auth C] MOL2 format, chain O [auth B] MOL2 format, chain D [auth A] MOL2 format, chain X [auth C]	D [auth A], O [auth B], X [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain D [auth A] Focus chain O [auth B] Focus chain X [auth C] Interactions & Density Focus chain D [auth A] Focus chain O [auth B] Focus chain X [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain AA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] G [auth A] AA [auth C], BA [auth C], CA [auth C], DA [auth C], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], R [auth B], S [auth B], T [auth B], U [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain EA [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B]	EA [auth C] FA [auth C] L [auth A] M [auth A] N [auth B] EA [auth C], FA [auth C], L [auth A], M [auth A], N [auth B], V [auth B], W [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain V [auth B] Focus chain W [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain Z [auth C] SDF format, chain Q [auth B] MOL2 format, chain F [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain Q [auth B]	F [auth A], Q [auth B], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain Q [auth B] Focus chain Z [auth C] Interactions & Density Focus chain F [auth A] Focus chain Q [auth B] Focus chain Z [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain P [auth B] SDF format, chain Y [auth C] MOL2 format, chain E [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Y [auth C]	E [auth A], P [auth B], Y [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain P [auth B] Focus chain Y [auth C] Interactions & Density Focus chain E [auth A] Focus chain P [auth B] Focus chain Y [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.164
R-Value Work: 0.150
R-Value Observed: 0.151
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.999	α = 90
b = 99.151	β = 103.27
c = 83.89	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-04-17

Deposition Author(s):

Ramirez-Escudero, M.

Sanz-Aparicio, J.

Revision History (Full details and data files)

Version 1.0: 2019-04-17
Type: Initial release
Version 1.1: 2020-04-29
Changes: Data collection, Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary