1YRZ | pdb_00001yrz

Crystal structure of xylan beta-1,4-xylosidase from Bacillus Halodurans C-125

• PDB DOI: https://doi.org/10.2210/pdb1YRZ/pdb

• Classification: HYDROLASE
• Organism(s): Halalkalibacterium halodurans C-125
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-02-05 Released: 2005-02-22 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.224 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Crystal Structure of xylan beta-1,4-xylosidase from Bacillus Halodurans C-125

Fedorov, A.A., Fedorov, E.V., Almo, S.C.

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: 121.12 kDa 
• Atom Count: 8,867 
• Modeled Residue Count: 1,044 
• Deposited Residue Count: 1,056 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
xylan beta-1,4-xylosidase	A, B	528	Halalkalibacterium halodurans C-125	Mutation(s): 0  EC: 3.2.1.37
UniProt
Find proteins for Q9K6P5 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9K6P5  Go to UniProtKB:  Q9K6P5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.224 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.063	α = 90
b = 125.817	β = 95.08
c = 97.131	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-22 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2005-02-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references