2CKR | pdb_00002ckr

X-RAY CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THERMOBIFIDA FUSCA ENDOGLUCANASE CEL5A (E5) E355Q IN COMPLEX WITH CELLOTETRAOSE

• PDB DOI: https://doi.org/10.2210/pdb2CKR/pdb

• Classification: HYDROLASE
• Organism(s): Thermobifida fusca
• Expression System: Bacillus subtilis
• Mutation(s): Yes 


• Deposited: 2006-04-21 Released: 2007-05-29 
• Deposition Author(s): Berglund, G.I., Gualfetti, P.J., Requadt, C., Gross, L.S., Bergfors, T., Shaw, A., Saldajeno, M., Mitchinson, C., Sandgren, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.193 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Literature

The Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase Cel5A in Complex with Cellotetraose

Berglund, G.I., Gualfetti, P.J., Requadt, C., Gross, L.S., Bergfors, T., Shaw, A., Saldajeno, M., Mitchinson, C., Sandgren, M.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 69.97 kDa 
• Atom Count: 5,687 
• Modeled Residue Count: 610 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDOGLUCANASE E-5	A, B	306	Thermobifida fusca	Mutation(s): 1  EC: 3.2.1.4
UniProt
Find proteins for Q01786 (Thermobifida fusca) Explore Q01786  Go to UniProtKB:  Q01786

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	C	5		N/A
Glycosylation Resources
GlyTouCan: G91683DU GlyCosmos: G91683DU

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
BEN	E [auth A], H [auth B]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
ZN	F [auth A], G [auth A], I [auth B], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900016	C	beta-cellopentaose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.193 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.365	α = 90
b = 70.85	β = 93.86
c = 76.278	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-29 
Deposition Author(s): Berglund, G.I., Gualfetti, P.J., Requadt, C., Gross, L.S., Bergfors, T., Shaw, A., Saldajeno, M., Mitchinson, C., Sandgren, M.

Revision History  

• Version 1.0: 2007-05-29
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2018-12-19
  Changes: Advisory, Atomic model, Data collection, Derived calculations
• Version 2.1: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 3.1: 2024-11-06
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary