3QHM

Crystal analysis of the complex structure, E342A-cellotetraose, of endocellulase from pyrococcus horikoshii

• PDB DOI: https://doi.org/10.2210/pdb3QHM/pdb

• Classification: HYDROLASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-01-26 Released: 2012-02-01 
• Deposition Author(s): Kim, H.-W., Ishikawa, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.261 
• R-Value Work: 0.228 
• R-Value Observed: 0.228 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 158.12 kDa 
• Atom Count: 9,565 
• Modelled Residue Count: 1,131 
• Deposited Residue Count: 1,374 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
458aa long hypothetical endo-1,4-beta-glucanase	A, B, C	458	Pyrococcus horikoshii	Mutation(s): 1  Gene Names: PH1171 EC: 3.2.1.4
UniProt
Find proteins for O58925 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58925  Go to UniProtKB:  O58925

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	D, E, G	4		N/A
Glycosylation Resources
GlyTouCan:  G00025MO GlyCosmos:  G00025MO GlyGen:  G00025MO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	F	2		N/A
Glycosylation Resources
GlyTouCan:  G84824ZO GlyCosmos:  G84824ZO

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900011	D, E, G	beta-cellotetraose	Oligosaccharide / Metabolism

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005	F	beta-cellobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.261 
• R-Value Work: 0.228 
• R-Value Observed: 0.228 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.535	α = 90
b = 58.598	β = 109.69
c = 139.063	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-01 
Deposition Author(s): Kim, H.-W., Ishikawa, K.

Revision History  

• Version 1.0: 2012-02-01
  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, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary