3RJA | pdb_00003rja

Crystal structure of carbohydrate oxidase from Microdochium nivale in complex with substrate analogue

• PDB DOI: https://doi.org/10.2210/pdb3RJA/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., Kolenko, P., Stepankova, A., Koval, T., Hasek, J., Ostergaard, L.H., Fuglsang, C.C., Dohnalek, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Work: 
  0.142 (Depositor) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

Crystal structure and kinetic studies of carbohydrate oxidase from Microdochium nivale

Duskova, J., Skalova, T., Kolenko, P., Stepankova, A., Hasek, J., Koval, T., 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: 54.71 kDa 
• Atom Count: 4,543 
• 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

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
ABL	G [auth A], H [auth A]	(2R,3R,4R,5R)-4,5-dihydroxy-2-(hydroxymethyl)-6-oxopiperidin-3-yl beta-D-glucopyranoside C12 H21 N O10 WXSNJJDPPISYEF-ZNLUKOTNSA-N
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
TRS	I [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4	J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	K [auth A], L [auth A], M [auth A], N [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Work:  0.142 (Depositor) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.04	α = 90
b = 56.92	β = 95.55
c = 86.9	γ = 90

Software Package:

Software Name	Purpose
CrysalisPro	data collection
MOLREP	phasing
REFMAC	refinement
CrysalisPro	data reduction
Jana2006	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2012-04-18
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: 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: 2024-11-06
  Changes: Structure summary