4GAK | pdb_00004gak

Crystal structure of acyl-ACP thioesterase from Spirosoma linguale

• PDB DOI: https://doi.org/10.2210/pdb4GAK/pdb

• Classification: HYDROLASE
• Organism(s): Spirosoma linguale DSM 74
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-07-25 Released: 2012-09-19 
• Deposition Author(s): Chang, C., Wu, R., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.224 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Crystal structure of acyl-ACP thioesterase from Spirosoma linguale

Chang, C., Wu, R., Endres, M., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 29.19 kDa 
• Atom Count: 2,261 
• Modeled Residue Count: 250 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl-ACP thioesterase	A	250	Spirosoma linguale DSM 74	Mutation(s): 0  Gene Names: Slin_6353
UniProt
Find proteins for D2QU30 (Spirosoma linguale (strain ATCC 33905 / DSM 74 / LMG 10896 / Claus 1)) Explore D2QU30  Go to UniProtKB:  D2QU30

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.224 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34GAK

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.657	α = 90
b = 61.657	β = 90
c = 155.945	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
ARP/wARP	model building
RESOLVE	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-19 
Deposition Author(s): Chang, C., Wu, R., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-09-19
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary