1TBU | pdb_00001tbu

Crystal structure of N-terminal domain of yeast peroxisomal thioesterase-1

• PDB DOI: https://doi.org/10.2210/pdb1TBU/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-05-20 Released: 2005-10-04 
• Deposition Author(s): Devedjiev, Y.D., Li, J., Derewenda, U., Derewenda, Z.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.260 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.215 (Depositor) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

Crystal structure of N-terminal domain of yeast peroxisomal thioesterase-1

Devedjiev, Y.D., Li, J., Derewenda, U., Derewenda, Z.S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 52.49 kDa 
• Atom Count: 3,213 
• Modeled Residue Count: 387 
• Deposited Residue Count: 472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisomal acyl-coenzyme A thioester hydrolase 1	A, B, C, D	118	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: PTE1, TES1, YJR019C, J1456 EC: 3.1.2.2
UniProt
Find proteins for P41903 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41903  Go to UniProtKB:  P41903

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	E [auth B], F [auth D]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.260 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.215 (Depositor) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.261	α = 90
b = 80.261	β = 90
c = 137.079	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SHELXD	phasing
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-04 
Deposition Author(s): Devedjiev, Y.D., Li, J., Derewenda, U., Derewenda, Z.S.

Revision History  

• Version 1.0: 2005-10-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations