5DPN | pdb_00005dpn

Engineered CBM X-2 L110F in complex with branched carbohydrate XXXG.

• PDB DOI: https://doi.org/10.2210/pdb5DPN/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Rhodothermus marinus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-09-13 Released: 2015-10-28 
• Deposition Author(s): Ohlin, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.250 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

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• Method: NEUTRON DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.204 (Depositor) 
• R-Value Work: 
  0.163 (Depositor) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Neutron Crystallographic Studies Reveal Hydrogen Bond and Water-Mediated Interactions between a Carbohydrate-Binding Module and Its Bound Carbohydrate Ligand.

Fisher, S.Z., von Schantz, L., Hakansson, M., Logan, D.T., Ohlin, M.

(2015) Biochemistry 54: 6435-6438

• PubMed: 26451738 
• DOI: https://doi.org/10.1021/acs.biochem.5b01058
• Primary Citation Related Structures: 
  5DPN


• PubMed Abstract: 
  

  Carbohydrate-binding modules (CBMs) are key components of many carbohydrate-modifying enzymes. CBMs affect the activity of these enzymes by modulating bonding and catalysis. To further characterize and study CBM-ligand binding interactions, neutron crystallographic studies of an engineered family 4-type CBM in complex with a branched xyloglucan ligand were conducted. The first neutron crystal structure of a CBM-ligand complex reported here shows numerous atomic details of hydrogen bonding and water-mediated interactions and reveals the charged state of key binding cleft amino acid side chains.

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Organizational Affiliation: 
• European Spallation Source , S-221 00 Lund, Sweden.
Department of Immunotechnology, Lund University , Medicon Village, S-223 81 Lund, Sweden.
SARomics Biostructures AB , Medicon Village, S-223 81 Lund, Sweden.
Department of Biochemistry and Structural Biology, Lund University , S-221 00 Lund, Sweden.

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: 19.04 kDa 
• Atom Count: 1,478 
• Modeled Residue Count: 166 
• Deposited Residue Count: 167 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylanase	A	167	Rhodothermus marinus	Mutation(s): 7  EC: 3.2.1.8
UniProt
Find proteins for Q7WTN6 (Rhodothermus marinus) Explore Q7WTN6  Go to UniProtKB:  Q7WTN6

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	B	7		N/A
Glycosylation Resources
GlyTouCan: G24181CY GlyCosmos: G24181CY

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.250 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

• Method: NEUTRON DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.204 (Depositor) 
• R-Value Work:  0.163 (Depositor) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.977	α = 90
b = 49.856	β = 90
c = 45.091	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-28 
Deposition Author(s): Ohlin, M.

Revision History  

• Version 1.0: 2015-10-28
  Type: Initial release
  
• Version 1.1: 2015-11-04
  Changes: Database references
• Version 1.2: 2018-01-17
  Changes: Data collection
• Version 1.3: 2018-02-28
  Changes: Data collection
• Version 1.4: 2018-03-07
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary