2ZUN | pdb_00002zun

Functional Analysis of Hyperthermophilic Endocellulase from the Archaeon Pyrococcus horikoshii

• PDB DOI: https://doi.org/10.2210/pdb2ZUN/pdb

• Classification: HYDROLASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-10-21 Released: 2009-11-03 
• Deposition Author(s): Kim, H.-W., Ishikawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.225 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.210 (DCC) 

Starting Model: experimental

Literature

Functional Analysis of Hyperthermophilic Endocellulase from the Archaeon Pyrococcus horikoshii

Kim, H.-W., Ishikawa, K.

To be published.

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: 158.2 kDa 
• Atom Count: 9,875 
• Modeled Residue Count: 1,134 
• 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 OT3	Mutation(s): 0  Gene Names: EGPh 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	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	D, E, F, G, H, I	2		N/A
Glycosylation Resources
GlyTouCan: G84824ZO GlyCosmos: G84824ZO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	J [auth A], K [auth A], L [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Biologically Interesting Molecules (External Reference) 

1 Unique

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.225 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.210 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.157	α = 90
b = 58.404	β = 109.22
c = 138.332	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASES	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-03 
Deposition Author(s): Kim, H.-W., Ishikawa, K.

Revision History  

• Version 1.0: 2009-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• 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: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary