7SKP | pdb_00007skp

De novo synthetic protein DIG14 (tetragonal space group)

PDB DOI: https://doi.org/10.2210/pdb7SKP/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: 2.50 Å
R-Value Free:
0.300 (Depositor), 0.271 (DCC)
R-Value Work:
0.247 (Depositor), 0.246 (DCC)
R-Value Observed:
0.249 (Depositor)

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

This is version 1.1 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: 19.62 kDa
Atom Count: 1,205
Modeled Residue Count: 146
Deposited Residue Count: 166
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo synthetic protein DIG14	A, B	83	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.300 (Depositor), 0.271 (DCC)
R-Value Work: 0.247 (Depositor), 0.246 (DCC)
R-Value Observed: 0.249 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.91	α = 90
b = 73.91	β = 90
c = 97.48	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-10-12

Deposition Author(s):

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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.