3MS8 | pdb_00003ms8

Enzyme-Substrate interactions of IXT6, the intracellular xylanase of G. stearothermophilus.

• PDB DOI: https://doi.org/10.2210/pdb3MS8/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-04-29 Released: 2011-05-11 
• Deposition Author(s): Solomon, V., Zolotnitsky, G., Alhadeff, R., Shoham, Y., Shoham, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.209 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.208 (DCC) 

Starting Model: experimental

Literature

Enzyme-Substrate interactions of IXT6, the intracellular xylanase of G. stearothermophilus.

Solomon, V., Zolotnitsky, G., Alhadeff, R., Shoham, Y., Shoham, G.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 77.87 kDa 
• Atom Count: 6,033 
• Modeled Residue Count: 658 
• Deposited Residue Count: 662 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Intra-cellular xylanase ixt6	A, B	331	Geobacillus stearothermophilus	Mutation(s): 1  Gene Names: xynA2 EC: 3.2.1.8
UniProt
Find proteins for Q09LY9 (Geobacillus stearothermophilus) Explore Q09LY9  Go to UniProtKB:  Q09LY9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	F [auth A], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.209 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.208 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.389	α = 90
b = 80.081	β = 91.5
c = 79.026	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-11 
Deposition Author(s): Solomon, V., Zolotnitsky, G., Alhadeff, R., Shoham, Y., Shoham, G.

Revision History  

• Version 1.0: 2011-05-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description