3JXS | pdb_00003jxs

Crystal structure of XG34, an evolved xyloglucan binding CBM

• PDB DOI: https://doi.org/10.2210/pdb3JXS/pdb

• Classification: hydrolase, carbohydrate-binding domain
• Organism(s): Rhodothermus marinus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-09-21 Released: 2009-10-27 
• Deposition Author(s): Divne, C., Tan, T.-C., Brumer, H., Gullfot, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.213 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of XG-34, an evolved xyloglucan-specific carbohydrate-binding module.

Gullfot, F., Tan, T.C., von Schantz, L., Karlsson, E.N., Ohlin, M., Brumer, H., Divne, C.

(2009) Proteins 78: 785-789

• PubMed: 19950365 
• DOI: https://doi.org/10.1002/prot.22642
• Primary Citation Related Structures: 
  3JXS

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Organizational Affiliation: 
• Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden.

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 57.04 kDa 
• Atom Count: 4,164 
• Modeled Residue Count: 498 
• Deposited Residue Count: 522 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylanase	A, B, C	174	Rhodothermus marinus	Mutation(s): 7  Gene Names: xg-34 EC: 3.2.1.8
UniProt
Find proteins for Q7WTN6 (Rhodothermus marinus) Explore Q7WTN6  Go to UniProtKB:  Q7WTN6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	G [auth B], J [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	D [auth A], E [auth A], F [auth B], H [auth C], I [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.213 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.57	α = 90
b = 43.76	β = 104.27
c = 93.08	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-27 
Deposition Author(s): Divne, C., Tan, T.-C., Brumer, H., Gullfot, F.

Revision History  

• Version 1.0: 2009-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Data collection, Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description