5M0K | pdb_00005m0k

CRYSTAL STRUCTURE of endo-1,4-beta-xylanase from Cellulomonas flavigena

• PDB DOI: https://doi.org/10.2210/pdb5M0K/pdb

• Classification: HYDROLASE
• Organism(s): Cellulomonas flavigena
• Expression System: Komagataella phaffii GS115
• Mutation(s): No 


• Deposited: 2016-10-05 Released: 2017-11-29 
• Deposition Author(s): Gabdulkhakov, A., Tishchenko, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 
  0.260 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE of endo-1,4-beta-xylanase from Cellulomonas flavigena

Gabdulkhakov, A., Tishchenko, S.

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: 77.53 kDa 
• Atom Count: 4,645 
• Modeled Residue Count: 598 
• Deposited Residue Count: 720 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylanase	A, B	360	Cellulomonas flavigena	Mutation(s): 0  Gene Names: Cfla_0376 EC: 3.2.1.8
UniProt
Find proteins for D5UH90 (Cellulomonas flavigena (strain ATCC 482 / DSM 20109 / BCRC 11376 / JCM 18109 / NBRC 3775 / NCIMB 8073 / NRS 134)) Explore D5UH90  Go to UniProtKB:  D5UH90

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.260 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.151	α = 90
b = 122.879	β = 92.52
c = 40.904	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-29 
Deposition Author(s): Gabdulkhakov, A., Tishchenko, S.

Revision History  

• Version 1.0: 2017-11-29
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary