5AG0 | pdb_00005ag0

DyP-type peroxidase of Auricularia auricula-judae (AauDyPI) crystallized at pH 6.5

PDB DOI: https://doi.org/10.2210/pdb5AG0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Auricularia auricula-judae
Mutation(s): No

Deposited: 2015-01-27 Released: 2016-03-09
Deposition Author(s): Strittmatter, E., Piontek, K., Plattner, D.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.222 (Depositor), 0.196 (DCC)
R-Value Work:
0.187 (Depositor)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.1 of the entry. See complete history.

Literature

Crystallographic Trapping of a Covalently Modified Heme in a Dye-Decolorizing Peroxidase

Strittmatter, E., Piontek, K., Plattner, D.A.

To be published.

Macromolecule Content

Total Structure Weight: 98.23 kDa
Atom Count: 7,634
Modeled Residue Count: 892
Deposited Residue Count: 892
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DYE-DECOLORIZING PEROXIDASE	A, B	446	Auricularia auricula-judae	Mutation(s): 0 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
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain T [auth B] MOL2 format, chain D [auth A] MOL2 format, chain T [auth B] mmCIF format, chain D [auth A] mmCIF format, chain T [auth B]	D [auth A], T [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain D [auth A] Focus chain T [auth B] Interactions & Density Focus chain D [auth A] Focus chain T [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth A], U [auth B], V [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain U [auth B] Focus chain V [auth B]
CAC Query on CAC Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain W [auth B] MOL2 format, chain G [auth A] MOL2 format, chain W [auth B] mmCIF format, chain G [auth A] mmCIF format, chain W [auth B]	G [auth A], W [auth B]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain W [auth B] Interactions & Density Focus chain G [auth A] Focus chain W [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain J [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain O [auth A] SDF format, chain L [auth A] SDF format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain O [auth A] MOL2 format, chain L [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain O [auth A] mmCIF format, chain L [auth A] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] J [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], J [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], Y [auth B], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain J [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain J [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
GOA Query on GOA Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	GLYCOLIC ACID C₂ H₄ O₃ AEMRFAOFKBGASW-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain H [auth A] SDF format, chain X [auth B] SDF format, chain I [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain X [auth B] MOL2 format, chain I [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain X [auth B] mmCIF format, chain I [auth A]	EA [auth B], H [auth A], I [auth A], X [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain X [auth B] Interactions & Density Focus chain EA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.222 (Depositor), 0.196 (DCC)
R-Value Work: 0.187 (Depositor)
R-Value Observed: 0.189 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.84	α = 90
b = 46.57	β = 100.49
c = 147.63	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-03-09

Deposition Author(s):

Strittmatter, E.

Piontek, K.

Plattner, D.A.

Revision History (Full details and data files)

Version 1.0: 2016-03-09
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 3.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Structure summary
Version 3.1: 2024-01-10
Changes: Refinement description