2YYZ | pdb_00002yyz

Crystal structure of Sugar ABC transporter, ATP-binding protein

• PDB DOI: https://doi.org/10.2210/pdb2YYZ/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-05-02 Released: 2007-11-06 
• Deposition Author(s): Ethayathullah, A.S., Bessho, Y., Padmanabhan, B., Singh, T.P., Kaur, P., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.280 (Depositor) 
• R-Value Work: 
  0.223 (Depositor) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Sugar ABC transporter, ATP-binding protein

Ethayathullah, A.S., Bessho, Y., Padmanabhan, B., Singh, T.P., Kaur, P., Yokoyama, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 40.74 kDa 
• Atom Count: 3,159 
• Modeled Residue Count: 358 
• Deposited Residue Count: 359 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar ABC transporter, ATP-binding protein	A	359	Thermotoga maritima MSB8	Mutation(s): 0
UniProt
Find proteins for Q9WYQ2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYQ2  Go to UniProtKB:  Q9WYQ2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.280 (Depositor) 
• R-Value Work:  0.223 (Depositor) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.063	α = 90
b = 86.774	β = 90
c = 105.681	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-06 
Deposition Author(s): Ethayathullah, A.S., Bessho, Y., Padmanabhan, B., Singh, T.P., Kaur, P., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-11-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description