5FIO | pdb_00005fio

DARPins as a new tool for experimental phasing in protein crystallography

• PDB DOI: https://doi.org/10.2210/pdb5FIO/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): synthetic construct, Escherichia coli
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2015-09-30 Released: 2016-11-16 
• Deposition Author(s): Batyuk, A., Honegger, A., Andres, F., Briand, C., Gruetter, M., Plueckthun, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.253 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Darpins as a New Tool for Experimental Phasing in Protein Crystallography

Batyuk, A., Honegger, A., Andres, F., Briand, C., Gruetter, M., Plueckthun, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 61.97 kDa 
• Atom Count: 4,239 
• Modeled Residue Count: 526 
• Deposited Residue Count: 567 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NI3C DARPIN MUTANT5 HG-SITE N1	A	172	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MALTOSE-BINDING PERIPLASMIC PROTEIN	B	395	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	C [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.253 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.61	α = 90
b = 43.79	β = 108.28
c = 82.42	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-16 
Deposition Author(s): Batyuk, A., Honegger, A., Andres, F., Briand, C., Gruetter, M., Plueckthun, A.

Revision History  

• Version 1.0: 2016-11-16
  Type: Initial release
  
• Version 1.1: 2016-11-30
  Changes: Derived calculations
• Version 2.0: 2019-10-23
  Changes: Atomic model, Data collection, Other
• Version 2.1: 2024-05-08
  Changes: Data collection, Database references, Derived calculations