3RJA

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Work: 0.142
R-Value Observed: 0.145

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.3 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 54.71 kDa
Atom Count: 4,543
Modelled Residue Count: 473
Deposited Residue Count: 473
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I1SB12
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ABL Query on ABL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	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		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
TRS Query on TRS 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]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	K [auth A], L [auth A], M [auth A], N [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Work: 0.142
R-Value Observed: 0.145
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-04-18

Deposition Author(s):

Revision History (Full details and data files)

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