3MMD | pdb_00003mmd

Crystal structure of the W241A mutant of xylanase from Geobacillus stearothermophilus T-6 (XT6) complexed with hydrolyzed xylopentaose

• PDB DOI: https://doi.org/10.2210/pdb3MMD/pdb

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


• Deposited: 2010-04-19 Released: 2011-04-27 
• Deposition Author(s): Solomon, V., Zolotnitsky, G., Feinberg, H., Tabachnikov, O., Shoham, Y., Shoham, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.236 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.221 (DCC) 

Starting Model: experimental

Literature

Structural-based rational mutagenesis of xylanases from G.stearothermophilus

Solomon, V., Zolotnitsky, G., Feinberg, H., Tabachnikov, O., 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)

Macromolecule Content 

• Total Structure Weight: 44.66 kDa 
• Atom Count: 3,461 
• Modeled Residue Count: 371 
• Deposited Residue Count: 379 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase	A	379	Geobacillus stearothermophilus	Mutation(s): 1  Gene Names: xynA EC: 3.2.1.8
UniProt
Find proteins for P40943 (Geobacillus stearothermophilus) Explore P40943  Go to UniProtKB:  P40943

Oligosaccharides

Help  

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

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	C	3		N/A
Glycosylation Resources
GlyTouCan: G87429QT GlyCosmos: G87429QT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A], F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

2 Unique

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

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900117	C	4beta-beta-xylotriose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.236 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.221 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.241	α = 90
b = 61.856	β = 119.2
c = 89.066	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-27 
Deposition Author(s): Solomon, V., Zolotnitsky, G., Feinberg, H., Tabachnikov, O., Shoham, Y., Shoham, G.

Revision History  

• Version 1.0: 2011-04-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-10-06
  Changes: Database references, Structure summary
• Version 2.2: 2023-09-06
  Changes: Data collection, Refinement description