6K55 | pdb_00006k55

Inactivated mutant (D140A) of Hyperthermophilic GH6 cellobiohydrolase II (HmCel6A) in complex with hexasaccharide

• PDB DOI: https://doi.org/10.2210/pdb6K55/pdb

• Classification: HYDROLASE
• Organism(s): Ardenticatenia bacterium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-28 Released: 2020-06-03 
• Deposition Author(s): Baba, S., Takeda, M., Okuma, J., Hirose, Y., Nishimura, A., Takata, M., Oda, K., Shibata, D., Kondo, Y., Kumasaka, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

A hyperthermophilic cellobiohydrolase mined from a hot spring metagenomic data

Takeda, M., Baba, S., Okuma, J., Hirose, Y., Nishimura, A., Takata, M., Oda, K., Shibata, D., Kondo, Y., Kumasaka, T.

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 Evidence: gel filtration

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: 144.17 kDa 
• Atom Count: 10,273 
• Modeled Residue Count: 1,284 
• Deposited Residue Count: 1,284 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucanase	A, B, C	428	Ardenticatenia bacterium	Mutation(s): 0  Gene Names: D6802_06765 EC: 3.2.1
UniProt
Find proteins for A0A4Y1YS11 (uncultured Chloroflexota bacterium) Explore A0A4Y1YS11  Go to UniProtKB:  A0A4Y1YS11

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	D, E, F	7		N/A
Glycosylation Resources
GlyTouCan: G73749NK GlyCosmos: G73749NK GlyGen: G73749NK

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.949	α = 90
b = 140.01	β = 101.06
c = 110.578	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-03 
Deposition Author(s): Baba, S., Takeda, M., Okuma, J., Hirose, Y., Nishimura, A., Takata, M., Oda, K., Shibata, D., Kondo, Y., Kumasaka, T.

Revision History  

• Version 1.0: 2020-06-03
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-10-23
  Changes: Structure summary