5IKD | pdb_00005ikd

Asymmetric sulfoxidation by engineering the heme pocket of a dye-decolorizing peroxidase

PDB DOI: https://doi.org/10.2210/pdb5IKD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Auricularia auricula-judae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-03-03 Released: 2016-07-13
Deposition Author(s): Romero, A., Davo-Siguero, I., Martinez, A.T.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.11 Å
R-Value Free:
0.158 (Depositor), 0.168 (DCC)
R-Value Work:
0.149 (Depositor), 0.158 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5IKD

Ligand Structure Quality Assessment

This is version 3.0 of the entry. See complete history.

Literature

Asymmetric sulfoxidation by engineering the heme pocket of a dye-decolorizing peroxidase

Linde, D., Canellas, M., Davo-Siguero, I., Romero, A., Lucas, F., Ruiz-Duenas, F.J., Guallar, V., Martinez, A.T.

(2016) Catal Sci Technol

DOI: https://doi.org/10.1039/c6cy00539j

Macromolecule Content

Total Structure Weight: 47.33 kDa
Atom Count: 3,929
Modeled Residue Count: 446
Deposited Residue Count: 446
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dye-decolorizing peroxidase	A	446	Auricularia auricula-judae	Mutation(s): 1 Gene Names: dyp1 EC: 1.11.1.19 (PDB Primary Data), 1.11.1.7 (UniProt)
UniProt
Find proteins for I2DBY1 (Auricularia auricula-judae) Explore I2DBY1 Go to UniProtKB: I2DBY1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I2DBY1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM 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]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.11 Å
R-Value Free: 0.158 (Depositor), 0.168 (DCC)
R-Value Work: 0.149 (Depositor), 0.158 (DCC)
R-Value Observed: 0.150 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.928	α = 90
b = 56.065	β = 97.03
c = 82.709	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-07-13

Deposition Author(s):

Davo-Siguero, I.

Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BFU2014-55448-P

Revision History (Full details and data files)

Version 1.0: 2016-07-13
Type: Initial release
Version 2.0: 2017-09-06
Changes: Atomic model, Author supporting evidence
Version 3.0: 2024-01-10
Changes: Atomic model, Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.