8PJV | pdb_00008pjv

Crystal structure of the computationally designed SAKe6DR protein

PDB DOI: https://doi.org/10.2210/pdb8PJV/pdb

Classification: UNKNOWN FUNCTION
Organism(s): synthetic construct
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2023-06-23 Released: 2024-07-10
Deposition Author(s): Wouters, S.M.L.
Funding Organization(s): Research Foundation - Flanders (FWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.14 Å
R-Value Free:
0.174 (Depositor), 0.170 (DCC)
R-Value Work:
0.158 (Depositor), 0.160 (DCC)
R-Value Observed:
0.159 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Computational design of the SAKe scaffold proteins

Wouters, S.M.L., Noguchi, H., Voet, A.R.D.

To be published.

Macromolecule Content

Total Structure Weight: 33.56 kDa
Atom Count: 2,502
Modeled Residue Count: 288
Deposited Residue Count: 310
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAKe6DR	A	310	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.14 Å
R-Value Free: 0.174 (Depositor), 0.170 (DCC)
R-Value Work: 0.158 (Depositor), 0.160 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.932	α = 90
b = 87.949	β = 90
c = 78.373	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-10

Deposition Author(s):

Wouters, S.M.L.

Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	1S89918N
Research Foundation - Flanders (FWO)	Belgium	G0F9316N
Research Foundation - Flanders (FWO)	Belgium	G051917N

Revision History (Full details and data files)

Version 1.0: 2024-07-10
Type: Initial release

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.