1VJQ | pdb_00001vjq

Designed protein based on backbone conformation of procarboxypeptidase-A (1AYE) with sidechains chosen for maximal predicted stability.

• PDB DOI: https://doi.org/10.2210/pdb1VJQ/pdb

• Classification: STRUCTURAL GENOMICS, DE NOVO PROTEIN
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-03-19 Released: 2004-03-30 
• Deposition Author(s): Merritt, E.A., Baker, D., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.291 (Depositor), 0.295 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.205 (DCC) 

Literature

Designed protein based on backbone conformation of procarboxypeptidase-A (1AYE) with sidechains chosen for maximal predicted stability.

Kuhlman, B., Dantas, G., Merritt, E.A., Baker, D.

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: 18.29 kDa 
• Atom Count: 1,243 
• Modeled Residue Count: 146 
• Deposited Residue Count: 158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
designed protein	A, B	79	N/A	Mutation(s): 0

Small Molecules

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: 2.10 Å
• R-Value Free:  0.291 (Depositor), 0.295 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.205 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.442	α = 90
b = 65.041	β = 90
c = 39.201	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
SHELX	phasing
RESOLVE	phasing
REFMAC	refinement
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-30 
Deposition Author(s): Merritt, E.A., Baker, D., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History  

• Version 1.0: 2004-03-30
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Structure summary