5I79 | pdb_00005i79

Crystal structure of a beta-1,4-endoglucanase mutant from Aspergillus niger in complex with sugar


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.208 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.147 (Depositor), 0.156 (DCC) 
  • R-Value Observed: 
    0.150 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Functional and structural analysis of Pichia pastoris-expressed Aspergillus niger 1,4-beta-endoglucanase

Yan, J.Liu, W.Li, Y.Lai, H.L.Zheng, Y.Huang, J.W.Chen, C.C.Chen, Y.Jin, J.Li, H.Guo, R.T.

(2016) Biochem Biophys Res Commun 475: 8-12

  • DOI: https://doi.org/10.1016/j.bbrc.2016.05.012
  • Primary Citation Related Structures: 
    5I77, 5I78, 5I79

  • PubMed Abstract: 

    Eukaryotic 1,4-β-endoglucanases (EC 3.2.1.4) have shown great potentials in many commercial applications because they effectively catalyze hydrolysis of cellulose, the main component of the plant cell wall. Here we expressed a glycoside hydrolase family (GH) 5 1,4-β-endoglucanase from Aspergillus niger (AnCel5A) in Pichia pastoris, which exhibits outstanding pH and heat stability. In order to further investigate the molecular mechanism of AnCel5A, apo-form and cellotetraose (CTT) complex enzyme crystal structures were solved to high resolution. AnCel5A folds into a typical (β/α)8-TIM barrel architecture, resembling other GH5 members. In the substrate binding cavity, CTT is found to bind to -4 - -1 subsites, and several polyethylene glycol molecules are found in positive subsites. In addition, several unique N-glycosylation motifs that may contribute to protein higher stability were observed from crystal structures. These results are of great importance for understanding the molecular mechanism of AnCel5A, and also provide guidance for further applications of the enzyme.


  • Organizational Affiliation
    • School of Biotechnology, Jiangnan University, Wuxi 214122, China.

Macromolecule Content 

  • Total Structure Weight: 70.21 kDa 
  • Atom Count: 5,180 
  • Modeled Residue Count: 606 
  • Deposited Residue Count: 608 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Endo-beta-1, 4-glucanase
A, B
304Aspergillus nigerMutation(s): 1 
Gene Names: eg1
EC: 3.2.1.4
UniProt
Find proteins for O74706 (Aspergillus niger)
Explore O74706 
Go to UniProtKB:  O74706
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO74706
Glycosylation
Glycosylation Sites: 1
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-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose
C, D
4N/A
Glycosylation Resources
GlyTouCan: G00025MO
GlyCosmos: G00025MO
GlyGen: G00025MO

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
F [auth A],
K [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
H [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
I [auth B],
J [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.147 (Depositor), 0.156 (DCC) 
  • R-Value Observed: 0.150 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.992α = 90
b = 51.332β = 95.2
c = 75.358γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, 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: 2024-10-30
    Changes: Structure summary