3W0K

Crystal Structure of a glycoside hydrolase

• PDB DOI: https://doi.org/10.2210/pdb3W0K/pdb

• Classification: HYDROLASE
• Organism(s): Caldanaerobius polysaccharolyticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-10-31 Released: 2013-02-20 
• Deposition Author(s): Oyama, T., Nakamura, H., Morikawa, K., Cann, I.K.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.188 
• R-Value Work: 0.176 
• R-Value Observed: 0.176 

Literature

Crystal structure of a glycoside hydrolase

Oyama, T., Schmitz, G.E., Dodd, D., Han, Y., Burnett, A., Nagasawa, N., Mackie, R.I., Nakamura, H., Morikawa, K., Cann, I.K.O.

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)

Macromolecule Content

• Total Structure Weight: 78.73 kDa 
• Atom Count: 6,099 
• Modelled Residue Count: 655 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional endomannanase/endoglucanase	A, B	330	Caldanaerobius polysaccharolyticus	Mutation(s): 0  Gene Names: man5B
UniProt
Find proteins for D9J0D7 (Caldanaerobius polysaccharolyticus) Explore D9J0D7  Go to UniProtKB:  D9J0D7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	C [auth A], D [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.188 
• R-Value Work: 0.176 
• R-Value Observed: 0.176 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.133	α = 90
b = 147.642	β = 104.51
c = 55.422	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-20 
Deposition Author(s): Oyama, T., Nakamura, H., Morikawa, K., Cann, I.K.O.

Revision History  

• Version 1.0: 2013-02-20
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description