2DEP | pdb_00002dep

Crystal Structure of xylanase B from Clostridium stercorarium F9

• PDB DOI: https://doi.org/10.2210/pdb2DEP/pdb

• Classification: HYDROLASE
• Organism(s): Thermoclostridium stercorarium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-02-16 Released: 2007-01-16 
• Deposition Author(s): Fushinobu, S., Nishimoto, M., Miyanaga, A., Kitaoka, M., Hayashi, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.210 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Molecular anatomy of the alkaliphilic xylanase from Bacillus halodurans C-125

Nishimoto, M., Fushinobu, S., Miyanaga, A., Kitaoka, M., Hayashi, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 82.73 kDa 
• Atom Count: 6,256 
• Modeled Residue Count: 679 
• Deposited Residue Count: 712 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermostable celloxylanase	A, B	356	Thermoclostridium stercorarium	Mutation(s): 0  Gene Names: xynB EC: 3.2.1.4 (PDB Primary Data), 3.2.1.8 (PDB Primary Data)
UniProt
Find proteins for P40942 (Thermoclostridium stercorarium) Explore P40942  Go to UniProtKB:  P40942

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.210 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.76	α = 90
b = 96.6	β = 90
c = 138.44	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-16 
Deposition Author(s): Fushinobu, S., Nishimoto, M., Miyanaga, A., Kitaoka, M., Hayashi, K.

Revision History  

• Version 1.0: 2007-01-16
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Refinement description