8HWP

Crystal Structure of Mutant GDSL Esterase of Photobacterium sp. J15 S12A in Complex with Butyrate

• PDB DOI: https://doi.org/10.2210/pdb8HWP/pdb

• Classification: HYDROLASE
• Organism(s): Photobacterium sp. J15
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-01-02 Released: 2023-06-28 
• Deposition Author(s): Rahman, N.N.A., Leow, T.C., Jonet, M.A.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.275 
• R-Value Work: 0.241 
• R-Value Observed: 0.242 

Starting Model: experimental

Literature

Crystal Structure of Mutant GDSL Esterase of Photobacterium sp. J15 in Complex with Butyrate

Rahman, N.N.A., Leow, T.C., Jonet, M.A.

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: 35.73 kDa 
• Atom Count: 2,521 
• Modelled Residue Count: 328 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDSL-family esterase	A	328	Photobacterium sp. J15	Mutation(s): 1
UniProt
Find proteins for A0A0K0PV22 (Photobacterium sp. J15(2011)) Explore A0A0K0PV22  Go to UniProtKB:  A0A0K0PV22

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BUA (Subject of Investigation/LOI)	B [auth A]	butanoic acid C4 H8 O2 FERIUCNNQQJTOY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.275 
• R-Value Work: 0.241 
• R-Value Observed: 0.242 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.007	α = 90
b = 56.626	β = 90
c = 119.678	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
iMOSFLM	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-28 
Deposition Author(s): Rahman, N.N.A., Leow, T.C., Jonet, M.A.

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Funding Organization	Location	Grant Number
Other government		--

Revision History  

• Version 1.0: 2023-06-28
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection