7SKO | pdb_00007sko

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

PDB DOI: https://doi.org/10.2210/pdb7SKO/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: 2.05 Å
R-Value Free:
0.291 (Depositor), 0.290 (DCC)
R-Value Work:
0.250 (Depositor), 0.251 (DCC)
R-Value Observed:
0.252 (Depositor)

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

Validation slider image for 7SKO

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: 33.28 kDa
Atom Count: 2,173
Modeled Residue Count: 283
Deposited Residue Count: 292
Unique protein chains: 1

Macromolecules

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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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.291 (Depositor), 0.290 (DCC)
R-Value Work: 0.250 (Depositor), 0.251 (DCC)
R-Value Observed: 0.252 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.03	α = 90
b = 76.52	β = 90
c = 165.8	γ = 90

Software Package:

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

Structure Validation

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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: 2024-11-13
Changes: Structure summary

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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.