7VTY | pdb_00007vty

de novo designed protein

• PDB DOI: https://doi.org/10.2210/pdb7VTY/pdb

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


• Deposited: 2021-10-31 Released: 2022-06-08 
• Deposition Author(s): Zhang, L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.275 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Rotamer-free protein sequence design based on deep learning and self-consistency.

Zhang, L.

(2023) Nat Comput Sci 

• DOI: https://doi.org/10.1038/s43588-022-00273-6

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 10.25 kDa 
• Atom Count: 715 
• Modeled Residue Count: 90 
• Deposited Residue Count: 90 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
de novo designed protein	A	90	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.275 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.035	α = 90
b = 56.035	β = 90
c = 95.075	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-08 
Deposition Author(s): Zhang, L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-06-08
  Type: Initial release
  
• Version 1.1: 2023-06-28
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description