5GM5 | pdb_00005gm5

Crystal structure of FI-CMCase from Aspergillus aculeatus F-50 in complex with cellobiose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 
    0.181 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.144 (Depositor) 
  • R-Value Observed: 
    0.146 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.2 of the entry. See complete history

Literature

Crystal structure and genetic modifications of FI-CMCase from Aspergillus aculeatus F-50

Huang, J.W.Liu, W.Lai, H.L.Cheng, Y.S.Zheng, Y.Li, Q.Sun, H.Kuo, C.J.Guo, R.T.Chen, C.C.

(2016) Biochem Biophys Res Commun 478: 565-572

  • DOI: https://doi.org/10.1016/j.bbrc.2016.07.101
  • Primary Citation Related Structures: 
    5GM3, 5GM4, 5GM5

  • PubMed Abstract: 

    Cellulose is the major component of the plant cell wall and the most abundant renewable biomass on earth, and its decomposition has proven to be very useful in many commercial applications. Endo-1,4-β-d-glucanase (EC 3.2.1.4; endoglucanase), which catalyzes the random hydrolysis of 1,4-β-glycosidic bonds of the cellulose main chain to cleave cellulose into smaller fragments, is the key cellulolytic enzyme. An endoglucanase isolated from Aspergillus aculeatus F-50 (FI-CMCase), which is classified into the glycoside hydrolase (GH) family 12, was demonstrated to be effectively expressed in the industrial strain Pichia pastoris. Here, the crystal structure and complex structures of P. pastoris-expressed FI-CMCase were solved to high resolution. The overall structure is analyzed and compared to other GH12 members. In addition, the substrate-surrounding residues were engineered to search for variants with improved enzymatic activity. Among 14 mutants constructed, one with two-fold increase in protein expression was identified, which possesses a potential to be further developed as a commercial enzyme product.


  • Organizational Affiliation
    • AsiaPac Biotechnology Co., Ltd, Dongguan 523808, China.

Macromolecule Content 

  • Total Structure Weight: 169.41 kDa 
  • Atom Count: 13,561 
  • Modeled Residue Count: 1,530 
  • Deposited Residue Count: 1,540 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Endoglucanase-1
A, B, C, D, E
A, B, C, D, E, F, G
220Aspergillus aculeatusMutation(s): 1 
EC: 3.2.1.4
UniProt
Find proteins for P22669 (Aspergillus aculeatus)
Explore P22669 
Go to UniProtKB:  P22669
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22669
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose
H, I, J, K
2N/A
Glycosylation Resources
GlyTouCan: G84824ZO
GlyCosmos: G84824ZO

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE

Query on EPE



Download:Ideal Coordinates CCD File
O [auth B]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
L [auth A]
M [auth B]
N [auth B]
P [auth C]
Q [auth D]
L [auth A],
M [auth B],
N [auth B],
P [auth C],
Q [auth D],
R [auth D],
S [auth E],
T [auth F],
U [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free:  0.181 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.144 (Depositor) 
  • R-Value Observed: 0.146 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.447α = 90
b = 85.567β = 91.87
c = 106.526γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-16
    Changes: Structure summary