7SKN

De novo synthetic protein DIG8-CC (tetragonal space group)

PDB DOI: https://doi.org/10.2210/pdb7SKN/pdb

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-10-21 Released: 2022-10-12
Deposition Author(s): Mendes, S.R., Eckhard, U., Marcos, E., Gomis-Ruth, F.X.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.301
R-Value Work: 0.263
R-Value Observed: 0.264

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

De novo design of immunoglobulin-like domains

Chidyausiku, T.M., Mendes, S.R., Klima, J.C., Nadal, M., Eckhard, U., Roel-Touris, J., Houliston, S., Guevara, T., Haddox, H.K., Moyer, A., Arrowsmith, C.H., Gomis-Ruth, F.X., Baker, D., Marcos, E.

(2022) Nat Commun 13: 5661

DOI: https://doi.org/10.1038/s41467-022-33004-6

Macromolecule Content

Total Structure Weight: 33.26 kDa
Atom Count: 2,338
Modelled Residue Count: 289
Deposited Residue Count: 292
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo synthetic protein DIG8-CC	A, B, C, D	73	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: 2.30 Å
R-Value Free: 0.301
R-Value Work: 0.263
R-Value Observed: 0.264
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.17	α = 90
b = 58.17	β = 90
c = 173.5	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-10-12

Deposition Author(s):

Gomis-Ruth, F.X.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-10-12
Type: Initial release
Version 1.1: 2024-04-03
Changes: Data collection, Refinement description
Version 1.2: 2024-11-06
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.