8R2P | pdb_00008r2p

YZwIdeal x16 a scaffold for cryo-EM of small proteins of interest crystallizing in space group 19 (P 21 21 21)

• PDB DOI: https://doi.org/10.2210/pdb8R2P/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-11-07 Released: 2024-11-13 
• Deposition Author(s): Moche, M., Friberg, O., Nygren, P.A., Nilvebrant, J.
• Funding Organization(s): Clas Groschinsky Memorial Fund, Sven and Dagmar Salens Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 
  0.230 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Engineered imaging scaffolds for cryo-EM of small proteins of interest.

Moche, M., Nygren, P.A., Nilvebrant, J.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 229.21 kDa 
• Atom Count: 16,262 
• Modeled Residue Count: 1,884 
• Deposited Residue Count: 2,092 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putrescine aminotransferase,Immunoglobulin G-binding protein A	A, B, C, D	523	Escherichia coli	Mutation(s): 1  Gene Names: patA, ygjG, b3073, JW5510, spa EC: 2.6.1.82 (PDB Primary Data), 2.6.1.29 (PDB Primary Data)
UniProt
Find proteins for P02976 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P02976  Go to UniProtKB:  P02976
Find proteins for P42588 (Escherichia coli (strain K12)) Explore P42588  Go to UniProtKB:  P42588
UniProt Groups	P02976P42588

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	E [auth A], F [auth B], G [auth C], H [auth D]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free:  0.230 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.26	α = 90
b = 196.76	β = 90
c = 208.053	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
STARANISO	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-11-13 
Deposition Author(s): Moche, M., Friberg, O., Nygren, P.A., Nilvebrant, J.

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Funding Organization	Location	Grant Number
Clas Groschinsky Memorial Fund	Sweden	M19380
Sven and Dagmar Salens Foundation	Sweden	--

Revision History  

• Version 1.0: 2024-11-13
  Type: Initial release