3WY6 | pdb_00003wy6

Structure of hyperthermophilic family 12 endocellulase (E197A) from Pyrococcus furiosus in complex with laminaribiose

• PDB DOI: https://doi.org/10.2210/pdb3WY6/pdb

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


• Deposited: 2014-08-20 Released: 2015-09-16 
• Deposition Author(s): Kataoka, M., Ishikawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.126 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.128 (Depositor) 

Literature

Structure of hyperthermophilic family 12 endocellulase (E197A) from Pyrococcus furiosus in complex with laminaribiose

Kataoka, M., 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)

Macromolecule Content 

• Total Structure Weight: 38.13 kDa 
• Atom Count: 2,623 
• Modeled Residue Count: 270 
• Deposited Residue Count: 319 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase A	A	319	Pyrococcus furiosus	Mutation(s): 1  Gene Names: eglA EC: 3.2.1.4
UniProt
Find proteins for Q9V2T0 (Pyrococcus furiosus) Explore Q9V2T0  Go to UniProtKB:  Q9V2T0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G36535HU GlyCosmos:  G36535HU

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHE	E [auth A], F [auth A], G [auth A], H [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
BGC	I [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
GOL	J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900024	B	beta-laminaribiose	Oligosaccharide / Antimicrobial

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.126 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.128 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.03	α = 90
b = 118.865	β = 90
c = 46.873	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-16 
Deposition Author(s): Kataoka, M., Ishikawa, K.

Revision History  

• Version 1.0: 2015-09-16
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2024-03-20
  Changes: Data collection, Database references, Structure summary