5FUK | pdb_00005fuk

Crystallization of a dimeric heme peroxygenase from the fungus Marasmius rotula

• PDB DOI: https://doi.org/10.2210/pdb5FUK/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.183 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Dimeric Heme Peroxygenase from Marasmius Rotula

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.09 kDa 
• Atom Count: 4,624 
• Modeled Residue Count: 468 
• Deposited Residue Count: 468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MROUPO	A, B	234	Marasmius rotula	Mutation(s): 0  EC: 1.11.2.1
UniProt
Find proteins for A0A023H437 (Marasmius rotula) Explore A0A023H437  Go to UniProtKB:  A0A023H437
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	5		N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	6		N-Glycosylation
Glycosylation Resources
GlyTouCan: G34442SS GlyCosmos: G34442SS GlyGen: G34442SS

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], K [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SNP	F [auth A], L [auth B]	1-(ISOPROPYLAMINO)-3-(1-NAPHTHYLOXY)-2-PROPANOL C16 H21 N O2 AQHHHDLHHXJYJD-AWEZNQCLSA-N
RNP	H [auth A], N [auth B]	(1E,2R)-1-(ISOPROPYLIMINO)-3-(1-NAPHTHYLOXY)PROPAN-2-OL C16 H19 N O2 LLOTXRYLQVWOGC-AYCSXLNKSA-N
PLM	G [auth A], M [auth B]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
NAG	J [auth A], P [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	Q [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	I [auth A], O [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.183 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.01	α = 90
b = 76.67	β = 90
c = 120.8	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-22 
Deposition Author(s): Piontek, K., Strittmatter, E., Plattner, D.A.

Revision History  

• Version 1.0: 2017-02-22
  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 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary