6H1Z | pdb_00006h1z

AFGH61B WILD-TYPE

PDB DOI: https://doi.org/10.2210/pdb6H1Z/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aspergillus fumigatus Af293
Expression System: Aspergillus oryzae
Mutation(s): No

Deposited: 2018-07-12 Released: 2018-08-22
Deposition Author(s): Lo Leggio, L., Poulsen, J.C.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free:
0.167 (Depositor), 0.175 (DCC)
R-Value Work:
0.129 (Depositor), 0.142 (DCC)
R-Value Observed:
0.131 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of a lytic polysaccharide monooxygenase from Aspergillus fumigatus and an engineered thermostable variant.

Lo Leggio, L., Weihe, C.D., Poulsen, J.N., Sweeney, M., Rasmussen, F., Lin, J., De Maria, L., Wogulis, M.

(2018) Carbohydr Res 469: 55-59

PubMed: 30296642 Search on PubMed
DOI: https://doi.org/10.1016/j.carres.2018.08.009
Primary Citation Related Structures:
6H1Z, 6HA5, 6HAQ

PubMed Abstract:
Lytic polysaccharide monooxygenases (LPMOs) are industrial enzymes which are gaining use in second generation bioethanol production from lignocellulose by acting in synergy with glycoside hydrolases. Here we present the X-ray crystal structure of an AA9 fungal LPMO from Aspergillus fumigatus and a variant which has been shown to have better performance at elevated temperatures. Based on the structures, thermal denaturation data and theoretical calculations, we provide a suggestion for the structural basis of the improved stability.

Organizational Affiliation

Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark. Electronic address: leila@chem.ku.dk.

Macromolecule Content

Total Structure Weight: 48.81 kDa
Atom Count: 4,022
Modeled Residue Count: 456
Deposited Residue Count: 458
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase, putative	A, B	229	Aspergillus fumigatus Af293	Mutation(s): 0 Gene Names: AFUA_4G07850 EC: 3.2.1 (PDB Primary Data), 1.14.99.54 (UniProt), 1.14.99.56 (UniProt)
UniProt
Find proteins for Q4WP32 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)) Explore Q4WP32 Go to UniProtKB: Q4WP32
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4WP32
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], I [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	D [auth A], E [auth A], F [auth A], G [auth A], J [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

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: 1.57 Å
R-Value Free: 0.167 (Depositor), 0.175 (DCC)
R-Value Work: 0.129 (Depositor), 0.142 (DCC)
R-Value Observed: 0.131 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.67	α = 89.62
b = 43.85	β = 108.33
c = 60.01	γ = 109.2

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-08-22

Deposition Author(s):

Lo Leggio, L.

Poulsen, J.C.N.

Revision History (Full details and data files)

Version 1.0: 2018-08-22
Type: Initial release
Version 1.1: 2018-10-17
Changes: Data collection, Database references
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description