3MSG | pdb_00003msg

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

• PDB DOI: https://doi.org/10.2210/pdb3MSG/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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: 1.50 Å
• R-Value Free: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (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: 78.64 kDa 
• Atom Count: 6,256 
• 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): 0  Gene Names: xynA2 EC: 3.2.1.8
UniProt
Find proteins for Q09LY9 (Geobacillus stearothermophilus) Explore Q09LY9  Go to UniProtKB:  Q09LY9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G87728WL GlyCosmos:  G87728WL

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XYP	E [auth A]	beta-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-KKQCNMDGSA-N
GOL	H [auth A], I [auth A], J [auth A], K [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	G [auth A], M [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	F [auth A], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900116	C, D	4beta-beta-xylobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.228	α = 90
b = 80.771	β = 91.73
c = 79.056	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: 2011-07-27
  Changes: Non-polymer description
• Version 1.3: 2017-11-15
  Changes: Advisory, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary