3V9A | pdb_00003v9a

Crystal structure of Esterase/Lipase from uncultured bacterium

• PDB DOI: https://doi.org/10.2210/pdb3V9A/pdb

• Classification: HYDROLASE ACTIVATOR
• Organism(s): uncultured bacterium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-12-24 Released: 2012-02-15 
• Deposition Author(s): Kim, I.J., Nam, K.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.239 (Depositor) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Crystal structure of Esterase/Lipase from uncultured bacterium

Kim, I.J., Nam, K.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 33.64 kDa 
• Atom Count: 2,335 
• Modeled Residue Count: 293 
• Deposited Residue Count: 309 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase/lipase	A	309	uncultured bacterium	Mutation(s): 0  Gene Names: estE5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.239 (Depositor) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.06	α = 90
b = 61.06	β = 90
c = 149.117	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-15 
Deposition Author(s): Kim, I.J., Nam, K.H.

Revision History  

• Version 1.0: 2012-02-15
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations