3RJ8 | pdb_00003rj8

Crystal structure of carbohydrate oxidase from Microdochium nivale

• PDB DOI: https://doi.org/10.2210/pdb3RJ8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Microdochium nivale
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 2011-04-15 Released: 2012-04-18 
• Deposition Author(s): Duskova, J., Skalova, T., Stepankova, A., Koval, T., Hasek, J., Ostergaard, L.H., Fuglsang, C.C., Kolenko, P., Dohnalek, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work: 
  0.155 (Depositor) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Crystal structure and kinetic studies of carbohydrate oxidase from Microdochium nivale

Duskova, J., Skalova, T., Kolenko, P., Stepankova, A., Koval, T., Hasek, J., Ostergaard, L.H., Fuglsang, C.C., Dohnalek, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 54.03 kDa 
• Atom Count: 4,209 
• Modeled Residue Count: 473 
• Deposited Residue Count: 473 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbohydrate oxidase	A	473	Microdochium nivale	Mutation(s): 0  Gene Names: MnCO EC: 1.1.3.5 (PDB Primary Data), 1.1.3 (UniProt)
UniProt
Find proteins for I1SB12 (Microdochium nivale) Explore I1SB12  Go to UniProtKB:  I1SB12
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

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	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
TRS	H [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
ZN	D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work:  0.155 (Depositor) 
• R-Value Observed: 0.156 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/796

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.71	α = 90
b = 56.96	β = 95.85
c = 87.05	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-18 
Deposition Author(s): Duskova, J., Skalova, T., Stepankova, A., Koval, T., Hasek, J., Ostergaard, L.H., Fuglsang, C.C., Kolenko, P., Dohnalek, J.

Revision History  

• Version 1.0: 2012-04-18
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Data collection, Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-02-22
  Changes: Database references, Structure summary
• Version 2.2: 2023-09-20
  Changes: Data collection, Refinement description
• Version 2.3: 2024-11-20
  Changes: Structure summary