4E88 | pdb_00004e88

CRYSTAL STRUCTURE OF DE NOVO DESIGNED CYSTEINE ESTERASE ECH13, Northeast Structural Genomics Consortium Target OR51

• PDB DOI: https://doi.org/10.2210/pdb4E88/pdb

• Classification: HYDROLASE
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2012-03-19 Released: 2012-04-11 
• Deposition Author(s): Kuzin, A., Su, M., Seetharaman, J., Xiao, X., Sahdev, S., Ciccosanti, C., Richter, F., Everett, J.K., Acton, T.B., 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: 2.00 Å
• R-Value Free: 
  0.215 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Northeast Structural Genomics Consortium Target OR51

Kuzin, A., Su, M., Seetharaman, J., Xiao, X., Sahdev, S., Ciccosanti, C., Richter, F., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

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)

Macromolecule Content

• Total Structure Weight: 24.3 kDa 
• Atom Count: 1,814 
• Modelled Residue Count: 195 
• Deposited Residue Count: 208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DE NOVO DESIGNED CYSTEINE ESTERASE ECH13	A	208	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.215 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.994	α = 90
b = 61.745	β = 128.95
c = 59.384	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-11 
Deposition Author(s): Kuzin, A., Su, M., Seetharaman, J., Xiao, X., Sahdev, S., Ciccosanti, C., Richter, F., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2012-04-11
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-11-06
  Changes: Structure summary