3K6K | pdb_00003k6k

Crystal structure at 2.2 angstrom of HSL-homolog EstE7 from a metagenome library

• PDB DOI: https://doi.org/10.2210/pdb3K6K/pdb

• Classification: HYDROLASE
• Organism(s): uncultured bacterium
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-10-09 Released: 2009-10-27 
• Deposition Author(s): Hwang, K.Y., Nam, K.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.282 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.223 (Depositor) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Biochemical and structural analysis of hormone-sensitive lipase homolog EstE7; Insight into the stabilized dimerization of HSL-homolog proteins

Nam, K.H., Rhee, K.H., Lee, W.H., Jeong, B.-C., Song, H.K., Hwang, K.Y.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 139.56 kDa 
• Atom Count: 9,335 
• Modeled Residue Count: 1,177 
• Deposited Residue Count: 1,288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase/lipase	A, B, C, D	322	uncultured bacterium	Mutation(s): 0  Gene Names: estE7 EC: 3.1.1
UniProt
Find proteins for A0ACD6B8C0 (uncultured bacterium) Explore A0ACD6B8C0  Go to UniProtKB:  A0ACD6B8C0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth C], K [auth C], L [auth D], M [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BME	N [auth D]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.282 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.223 (Depositor) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.157	α = 90
b = 127.699	β = 90
c = 232.87	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-27 
Deposition Author(s): Hwang, K.Y., Nam, K.H.

Revision History  

• Version 1.0: 2009-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description