1VJQ

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
R-Value Work: 0.199

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 18.29 kDa
Atom Count: 1,243
Modelled Residue Count: 146
Deposited Residue Count: 158
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
designed protein	A, B	79	N/A	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.199
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-03-30

Deposition Author(s):

Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.