3NDZ | pdb_00003ndz

The structure of the catalytic and carbohydrate binding domain of endoglucanase D from Clostridium cellulovorans bound to cellotriose

• PDB DOI: https://doi.org/10.2210/pdb3NDZ/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium cellulovorans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-08 Released: 2011-06-29 
• Deposition Author(s): Bianchetti, C.M., Smith, R.W., Bingman, C.A., Phillips Jr., G.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Literature

The structure of the catalytic and carbohydrate binding domain of endoglucanase D bound to cellotriose

Bianchetti, C.M., Smith, R.W., Bingman, C.A., Phillips Jr., G.N.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 

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

Macromolecule Content 

• Total Structure Weight: 201.36 kDa 
• Atom Count: 16,122 
• Modeled Residue Count: 1,808 
• Deposited Residue Count: 1,808 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase D	A, C [auth B], E [auth C], G [auth D]	345	Clostridium cellulovorans	Mutation(s): 0  Gene Names: engD EC: 3.2.1.4
UniProt
Find proteins for P28623 (Clostridium cellulovorans (strain ATCC 35296 / DSM 3052 / OCM 3 / 743B)) Explore P28623  Go to UniProtKB:  P28623

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase D	B [auth E], D [auth F], F [auth G], H	107	Clostridium cellulovorans	Mutation(s): 0  Gene Names: engD EC: 3.2.1.4
UniProt
Find proteins for P28623 (Clostridium cellulovorans (strain ATCC 35296 / DSM 3052 / OCM 3 / 743B)) Explore P28623  Go to UniProtKB:  P28623

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	I, J, K, L, M, N	3		N/A
Glycosylation Resources
GlyTouCan:  G14338VK GlyCosmos:  G14338VK GlyGen:  G14338VK

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900021	I, J, K, L, M, N	beta-cellotriose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.297	α = 90
b = 119.05	β = 90
c = 198.487	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-29 
Deposition Author(s): Bianchetti, C.M., Smith, R.W., Bingman, C.A., Phillips Jr., G.N.

Revision History  

• Version 1.0: 2011-06-29
  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: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-02-21
  Changes: Data collection, Database references, Structure summary