5DWD | pdb_00005dwd

Crystal structure of esterase PE8

• PDB DOI: https://doi.org/10.2210/pdb5DWD/pdb

• Classification: HYDROLASE
• Organism(s): Pelagibacterium halotolerans B2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-09-22 Released: 2016-10-26 
• Deposition Author(s): Li, J., Huang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Literature

Structure of esterase PE8

Li, J., Huang, J.

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.

Macromolecule Content 

• Total Structure Weight: 51.4 kDa 
• Atom Count: 3,579 
• Modeled Residue Count: 438 
• Deposited Residue Count: 480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase	A, B	240	Pelagibacterium halotolerans B2	Mutation(s): 0  Gene Names: KKY_2995 EC: 3.1.1.1
UniProt
Find proteins for G4RFI7 (Pelagibacterium halotolerans (strain DSM 22347 / JCM 15775 / CGMCC 1.7692 / B2)) Explore G4RFI7  Go to UniProtKB:  G4RFI7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PG	C [auth B]	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL C11 H24 O6 SLNYBUIEAMRFSZ-UHFFFAOYSA-N
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.772	α = 90
b = 73.398	β = 102.37
c = 66.403	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-26 
Deposition Author(s): Li, J., Huang, J.

Revision History  

• Version 1.0: 2016-10-26
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations