6F5N | pdb_00006f5n

Nickel-Bound Crystal Structure of a GB1 Variant

• PDB DOI: https://doi.org/10.2210/pdb6F5N/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Streptococcus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-12-01 Released: 2018-12-12 
• Deposition Author(s): Rothlisberger, U., Bozkurt, E., Hovius, R., Perez, M.A.S., Browning, N.J.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.356 (Depositor), 0.360 (DCC) 
• R-Value Work: 
  0.257 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.267 (Depositor) 

Starting Model: experimental

Literature

Nickel-Mediated Self-Assembly of an Ultrastable GB1 Variant

Bozkurt, E., Hovius, R., Browning, N.J., Perez, M.A.S., Rothlisberger, U.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 12.8 kDa 
• Atom Count: 974 
• Modeled Residue Count: 112 
• Deposited Residue Count: 112 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nickel-Binding Protein	A, B	56	Streptococcus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI (Subject of Investigation/LOI)	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.356 (Depositor), 0.360 (DCC) 
• R-Value Work:  0.257 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.267 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.68	α = 90
b = 59.328	β = 90
c = 75.729	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
ADDREF	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-12-12 
Deposition Author(s): Rothlisberger, U., Bozkurt, E., Hovius, R., Perez, M.A.S., Browning, N.J.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	200020-165863

Revision History  

• Version 1.0: 2018-12-12
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description