6TBR | pdb_00006tbr

Glycosylated AA13 Lytic polysaccharide monooxygenase from Aspergillus oryzae in P1 space group

PDB DOI: https://doi.org/10.2210/pdb6TBR/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aspergillus oryzae RIB40
Expression System: Aspergillus oryzae
Mutation(s): No

Deposited: 2019-11-04 Released: 2020-03-18
Deposition Author(s): Frandsen, K.E.H., Muderspach, S.J., Tandrup, T., Poulsen, J.C.N., Lo Leggio, L.
Funding Organization(s): Novo Nordisk Foundation, Danish Council for Independent Research, European Communitys Seventh Framework Programme

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.246 (Depositor), 0.251 (DCC)
R-Value Work:
0.192 (Depositor), 0.201 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Further structural studies of the lytic polysaccharide monooxygenase AoAA13 belonging to the starch-active AA13 family

Muderspach, S.J., Tandrup, T., Frandsen, K.E.H., Santoni, G., Poulsen, J.C.N., Lo Leggio, L.

(2019) Amylase 3(1): 41-54

DOI: https://doi.org/10.1515/amylase-2019-0004

Macromolecule Content

Total Structure Weight: 52.17 kDa
Atom Count: 4,255
Modeled Residue Count: 466
Deposited Residue Count: 466
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AoAA13	A, B	233	Aspergillus oryzae RIB40	Mutation(s): 0 Gene Names: AO090701000246
UniProt
Find proteins for Q2U8Y3 (Aspergillus oryzae (strain ATCC 42149 / RIB 40)) Explore Q2U8Y3 Go to UniProtKB: Q2U8Y3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2U8Y3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC Query on HIC	A, B	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.246 (Depositor), 0.251 (DCC)
R-Value Work: 0.192 (Depositor), 0.201 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.06	α = 109.37
b = 49.76	β = 90.07
c = 57.1	γ = 95.46

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-03-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF17SA0027704
Danish Council for Independent Research	Denmark	8021-00273B
European Communitys Seventh Framework Programme	Denmark	N283570

Revision History (Full details and data files)

Version 1.0: 2020-03-18
Type: Initial release
Version 1.1: 2025-04-09
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary

6TBR | pdb_00006tbr

Glycosylated AA13 Lytic polysaccharide monooxygenase from Aspergillus oryzae in P1 space group

Literature

Further structural studies of the lytic polysaccharide monooxygenase AoAA13 belonging to the starch-active AA13 family

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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