3FJW | pdb_00003fjw

Crystal Structure Analysis of Fungal Versatile Peroxidase from Pleurotus eryngii

PDB DOI: https://doi.org/10.2210/pdb3FJW/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pleurotus eryngii
Mutation(s): No

Deposited: 2008-12-15 Released: 2009-12-15
Deposition Author(s): Piontek, K., Martinez, A.T., Choinowski, T., Plattner, D.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.246 (Depositor), 0.245 (DCC)
R-Value Work:
0.158 (Depositor), 0.159 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Structural and Site-directed Mutagenesis Study of Versatile Peroxidase Oxidizing both Mn(II) and Aromatic Substrates

Piontek, K., Choinowski, T., Perez-Boada, M., Ruiz-Duenas, F.J., Martinez, M.J., Plattner, D.A., Martinez, A.T.

To be published.

Macromolecule Content

Total Structure Weight: 72.92 kDa
Atom Count: 5,548
Modeled Residue Count: 662
Deposited Residue Count: 662
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Versatile peroxidase VPL2	A, B	331	Pleurotus eryngii	Mutation(s): 0 EC: 1.11.1.16
UniProt
Find proteins for O94753 (Pleurotus eryngii) Explore O94753 Go to UniProtKB: O94753
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O94753
Glycosylation
Glycosylation Sites: 5	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
alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose	C, D	2		N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G09507TI GlyCosmos: G09507TI GlyGen: G09507TI

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 M [auth B] SDF format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain E [auth A]	E [auth A], M [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain M [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain I [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain I [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain I [auth A]	I [auth A], Q [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain Q [auth B] Interactions & Density Focus chain I [auth A] Focus chain Q [auth B]
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain R [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain R [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain R [auth B]	J [auth A] K [auth A] L [auth A] R [auth B] S [auth B] J [auth A], K [auth A], L [auth A], R [auth B], S [auth B], T [auth B]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain P [auth B] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B] mmCIF format, chain H [auth A] mmCIF format, chain P [auth B]	H [auth A], P [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain P [auth B] Interactions & Density Focus chain H [auth A] Focus chain P [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain F [auth A]	F [auth A], G [auth A], N [auth B], O [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.246 (Depositor), 0.245 (DCC)
R-Value Work: 0.158 (Depositor), 0.159 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.141	α = 90
b = 92.762	β = 90
c = 113.278	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-12-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-12-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-30
Changes: Structure summary