5EBA | pdb_00005eba

Crystal structure of aromatic mutant (Y343A) of an alkali thermostable GH10 xylanase from Bacillus sp. NG-27

• PDB DOI: https://doi.org/10.2210/pdb5EBA/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus sp. NG-27
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-10-18 Released: 2016-10-19 
• Deposition Author(s): Mahanta, P., Bhardwaj, A., Reddy, V.S., Ramakumar, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of aromatic mutant (Y343A) of an alkali thermostable GH10 xylanase from Bacillus sp. NG-27

Mahanta, P., Bhardwaj, A., Reddy, V.S., Ramakumar, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.07 kDa 
• Atom Count: 3,053 
• Modeled Residue Count: 354 
• Deposited Residue Count: 355 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylanase	A	355	Bacillus sp. NG-27	Mutation(s): 1  EC: 3.2.1.8
UniProt
Find proteins for O30700 (Bacillus sp. NG-27) Explore O30700  Go to UniProtKB:  O30700

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.86	α = 90
b = 80.11	β = 111.19
c = 69.21	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALA	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-19 
Deposition Author(s): Mahanta, P., Bhardwaj, A., Reddy, V.S., Ramakumar, S.

Revision History  

• Version 1.0: 2016-10-19
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description