7E16 | pdb_00007e16

crystal structure of GDSL esterase from Geobacillus thermodenitrificans

• PDB DOI: https://doi.org/10.2210/pdb7E16/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus thermodenitrificans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-01-31 Released: 2021-04-14 
• Deposition Author(s): Chen, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 
  0.278 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

Rational engineering of substrate selectivity of GDSL esterase from Geobacillus thermodenitrificans

Zhang, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 58.7 kDa 
• Atom Count: 3,262 
• Modeled Residue Count: 414 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDSL-family esterase	A, B	263	Geobacillus thermodenitrificans	Mutation(s): 0
UniProt
Find proteins for B2ZAB3 (Geobacillus thermodenitrificans) Explore B2ZAB3  Go to UniProtKB:  B2ZAB3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free:  0.278 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.424	α = 90
b = 106.424	β = 90
c = 128.643	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-14 
Deposition Author(s): Chen, L.

Revision History  

• Version 1.0: 2021-04-14
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description