5FUJ | pdb_00005fuj

Crystallization of a dimeric heme peroxygenase from the fungus Marasmius rotula

PDB DOI: https://doi.org/10.2210/pdb5FUJ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Marasmius rotula
Mutation(s): No

Deposited: 2016-01-27 Released: 2017-02-22
Deposition Author(s): Piontek, K., Strittmatter, E., Plattner, D.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.190 (Depositor), 0.190 (DCC)
R-Value Work:
0.155 (Depositor), 0.155 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystallization of a Dimeric Heme Peroxygenase

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

To be published.

Macromolecule Content

Total Structure Weight: 54.37 kDa
Atom Count: 4,376
Modeled Residue Count: 472
Deposited Residue Count: 472
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MROUPO	A, B	236	Marasmius rotula	Mutation(s): 0 EC: 1.11.2.1
UniProt
Find proteins for A0A023H437 (Marasmius rotula) Explore A0A023H437 Go to UniProtKB: A0A023H437
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A023H437
Glycosylation
Glycosylation Sites: 1	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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
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	D	3		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B], M [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	H [auth A], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.190 (Depositor), 0.190 (DCC)
R-Value Work: 0.155 (Depositor), 0.155 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.495	α = 90
b = 75.698	β = 90
c = 104.43	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: 2017-02-22

Deposition Author(s):

Piontek, K.

Strittmatter, E.

Plattner, D.A.

Revision History (Full details and data files)

Version 1.0: 2017-02-22
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-09
Changes: Structure summary