7DNS | pdb_00007dns

Crystal structure of domain-swapped dimer of H5_Fold-0 Elsa; de novo designed protein with an asymmetric all-alpha topology

PDB DOI: https://doi.org/10.2210/pdb7DNS/pdb

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

Deposited: 2020-12-10 Released: 2021-07-28
Deposition Author(s): Suzuki, K., Kobayashi, N., Murata, T., Sakuma, K., Kosugi, T., Koga, R., Koga, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.247 (Depositor), 0.256 (DCC)
R-Value Work:
0.207 (Depositor), 0.211 (DCC)
R-Value Observed:
0.209 (Depositor)

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Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Design of complicated all-alpha protein structures

Sakuma, K., Kobayashi, N., Sugiki, T., Nagashima, T., Fujiwara, T., Suzuki, K., Kobayashi, N., Murata, T., Kosugi, T., Koga, R., Koga, N.

(2024) Nat Struct Mol Biol

DOI: https://doi.org/10.1038/s41594-023-01147-9

Macromolecule Content

Total Structure Weight: 22.5 kDa
Atom Count: 1,443
Modeled Residue Count: 178
Deposited Residue Count: 194
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
de novo designed protein	A, B	97	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.247 (Depositor), 0.256 (DCC)
R-Value Work: 0.207 (Depositor), 0.211 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.98	α = 90
b = 33.66	β = 93.11
c = 58.38	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-07-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-07-28
Type: Initial release
Version 2.0: 2021-10-06
Changes: Advisory, Atomic model, Database references, Derived calculations, Experimental preparation, Polymer sequence, Source and taxonomy, Structure summary
Version 2.1: 2023-11-01
Changes: Data collection, Database references
Version 2.2: 2024-01-10
Changes: Database references

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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.