4PMD

Crystal structure of CbXyn10B from Caldicellulosiruptor bescii and its mutant(E139A) in complex with hydrolyzed xylotetraose

• PDB DOI: https://doi.org/10.2210/pdb4PMD/pdb

• Classification: HYDROLASE
• Organism(s): Caldicellulosiruptor bescii DSM 6725
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-05-21 Released: 2015-06-24 
• Deposition Author(s): An, J., Feng, Y., Wu, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.212 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Literature

Crystal structure of CbXyn10B from Caldicellulosiruptor bescii and its mutant(E139A) in complex with hydrolyzed xylotetraose

An, J., Wu, G., Feng, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.59 kDa 
• Atom Count: 2,938 
• Modelled Residue Count: 329 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase	A	338	Caldicellulosiruptor bescii DSM 6725	Mutation(s): 1  Gene Names: Athe_0185 EC: 3.2.1.8
UniProt
Find proteins for B9MMA5 (Caldicellulosiruptor bescii (strain ATCC BAA-1888 / DSM 6725 / KCTC 15123 / Z-1320)) Explore B9MMA5  Go to UniProtKB:  B9MMA5

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G87728WL GlyCosmos:  G87728WL

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900116	B	4beta-beta-xylobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.212 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.319	α = 90
b = 80.817	β = 90
c = 115.19	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-24 
Deposition Author(s): An, J., Feng, Y., Wu, G.

Revision History  

• Version 1.0: 2015-06-24
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
• Version 2.1: 2024-03-20
  Changes: Data collection, Database references, Structure summary