3C6Q

Apo and ligand-bound form of a thermophilic glucose/xylose binding protein

• PDB DOI: https://doi.org/10.2210/pdb3C6Q/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2008-02-05 Released: 2008-02-26 
• Deposition Author(s): Cuneo, M.J., Hellinga, H.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.281 
• R-Value Work: 0.214 

Starting Model: experimental

Literature

Open to closed transition of a thermophilic glucose binding protein

Cuneo, M.J., Hellinga, H.W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 135.13 kDa 
• Atom Count: 9,588 
• Modelled Residue Count: 1,220 
• Deposited Residue Count: 1,244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar ABC transporter, periplasmic sugar-binding protein	A [auth B], B [auth A], C, D	311	Thermotoga maritima	Mutation(s): 2  Gene Names: TM0114
UniProt
Find proteins for Q9WXW9 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WXW9  Go to UniProtKB:  Q9WXW9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XYP	E [auth C], F [auth D]	beta-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-KKQCNMDGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.281 
• R-Value Work: 0.214 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.1	α = 90
b = 75.75	β = 89.9
c = 100.52	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-26 
Deposition Author(s): Cuneo, M.J., Hellinga, H.W.

Revision History  

• Version 1.0: 2008-02-26
  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: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2021-10-20
  Changes: Database references, Structure summary
• Version 2.2: 2023-08-30
  Changes: Data collection, Refinement description