4JXI | pdb_00004jxi

Directed evolution and rational design of a de novo designed esterase toward improved catalysis. Northeast Structural Genomics Consortium (NESG) Target OR184

• PDB DOI: https://doi.org/10.2210/pdb4JXI/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2013-03-28 Released: 2013-05-22 
• Deposition Author(s): Kuzin, A., Smith, M.D., Richter, F., Lew, S., Seetharaman, R., Bryan, C., Lech, Z., Kiss, G., Moretti, R., Maglaqui, M., Xiao, R., Kohan, E., Smith, M., Everett, J.K., Nguyen, R., Pande, V., Hilvert, D., Kornhaber, G., Baker, D., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.232 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Directed evolution and rational design of a de novo designed esterase toward improved catalysis. Northeast Structural Genomics Consortium (NESG) Target OR184

Kuzin, A., Smith, M.D., Richter, F., Lew, S., Seetharaman, R., Bryan, C., Lech, Z., Kiss, G., Moretti, R., Maglaqui, M., Xiao, R., Kohan, E., Smith, M., Everett, J.K., Nguyen, R., Pande, V., Hilvert, D., Kornhaber, G., Baker, D., Montelione, G.T., Hunt, J.F., Tong, L.

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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 97.94 kDa 
• Atom Count: 6,996 
• Modeled Residue Count: 815 
• Deposited Residue Count: 838 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
design cystein esterase	A, B	419	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE5	I [auth B]	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL C18 H38 O9 CUDPPTPIUWYGFI-UHFFFAOYSA-N
GOL	H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BR	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.232 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.201	α = 90
b = 90.122	β = 90
c = 137.349	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-22 
Deposition Author(s): Kuzin, A., Smith, M.D., Richter, F., Lew, S., Seetharaman, R., Bryan, C., Lech, Z., Kiss, G., Moretti, R., Maglaqui, M., Xiao, R., Kohan, E., Smith, M., Everett, J.K., Nguyen, R., Pande, V., Hilvert, D., Kornhaber, G., Baker, D., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2013-05-22
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-11-27
  Changes: Structure summary