5YXT | pdb_00005yxt

Crystal structure of reducing end xylose-releasing exo-oligoxylanase

• PDB DOI: https://doi.org/10.2210/pdb5YXT/pdb

• Classification: HYDROLASE
• Organism(s): Paenibacillus barengoltzii G22
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-12-07 Released: 2018-12-12 
• Deposition Author(s): Jiang, Z.Q., You, X., Huang, P., Ma, J.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.289 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Starting Model: experimental

Literature

Structure of glycoside hydrolase family 8 xylanase at 1.88 Angstroms resolution

Jiang, Z.Q., You, X., Huang, P., Ma, J.W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 176.37 kDa 
• Atom Count: 13,190 
• Modeled Residue Count: 1,516 
• Deposited Residue Count: 1,528 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reducing end xylose-releasing exo-oligoxylanase	A, B, C, D	382	Paenibacillus barengoltzii G22	Mutation(s): 0  Gene Names: C812_03928
UniProt
Find proteins for R9L536 (Paenibacillus barengoltzii G22) Explore R9L536  Go to UniProtKB:  R9L536

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.289 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.57	α = 100.34
b = 78.99	β = 95.86
c = 89.148	γ = 106.35

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-12 
Deposition Author(s): Jiang, Z.Q., You, X., Huang, P., Ma, J.W.

Revision History  

• Version 1.0: 2018-12-12
  Type: Initial release
  
• Version 1.1: 2022-11-16
  Changes: Database references, Refinement description, Structure summary
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary