4RY8 | pdb_00004ry8

Crystal structure of 5-methylthioribose transporter solute binding protein TLET_1677 from Thermotoga lettingae TMO TARGET EFI-511109 in complex with 5-methylthioribose

• PDB DOI: https://doi.org/10.2210/pdb4RY8/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Pseudothermotoga lettingae TMO
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-13 Released: 2014-12-24 
• Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al obaidi, N., Morisco, L.L., Wasserman, S.R., Chamala, S., Attonito, J.D., Scott glenn, A., Chowdhury, S., Lafleur, J., Hillerich, B., Siede, R.D., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.264 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

Crystal structure of 5-methylthioribose binding protein TLET_1677 from Thermotoga lettingae TARGET EFI-511109

Patskovsky, Y., Toro, R., Bhosle, R., Al obaidi, N., Chamala, S., Scott glenn, A., Attonito, J.D., Chowdhury, S., Lafleur, J., Siedel, R.D., Morisco, L.L., Wasserman, S.R., Hillerich, B., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 147.07 kDa 
• Atom Count: 10,412 
• Modeled Residue Count: 1,276 
• Deposited Residue Count: 1,316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic binding protein	A, B, C, D	329	Pseudothermotoga lettingae TMO	Mutation(s): 0  Gene Names: Tlet_1677
UniProt
Find proteins for A8F7U7 (Pseudothermotoga lettingae (strain ATCC BAA-301 / DSM 14385 / NBRC 107922 / TMO)) Explore A8F7U7  Go to UniProtKB:  A8F7U7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SR1	E [auth A], F [auth B], G [auth C], H [auth D]	5-S-methyl-5-thio-alpha-D-ribofuranose C6 H12 O4 S OLVVOVIFTBSBBH-KAZBKCHUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.264 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.622	α = 91.83
b = 67.848	β = 92.39
c = 83.653	γ = 89.93

Software Package:

Software Name	Purpose
SHELX	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-24 
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al obaidi, N., Morisco, L.L., Wasserman, S.R., Chamala, S., Attonito, J.D., Scott glenn, A., Chowdhury, S., Lafleur, J., Hillerich, B., Siede, R.D., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2014-12-24
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Structure summary
• 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: 2024-02-28
  Changes: Data collection, Database references, Structure summary