5BU7 | pdb_00005bu7

Crystal structure of an engineered protein that forms nanotubes with tunable diameters

• PDB DOI: https://doi.org/10.2210/pdb5BU7/pdb

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


• Deposited: 2015-06-03 Released: 2016-06-08 
• Deposition Author(s): Brodin, J.D., Smith, S.J., Tezcan, F.A.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.292 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Designed, Helical Protein Nanotubes with Tunable Diameters from a Single Building Block.

Brodin, J.D., Smith, S.J., Tezcan, F.A.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.92 kDa 
• Atom Count: 1,765 
• Modeled Residue Count: 212 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562	A, B	106	Escherichia coli	Mutation(s): 15  Gene Names: cybC
UniProt
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], H [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
ZN	D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.292 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.89	α = 90
b = 52.89	β = 90
c = 257.08	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-06-08 
Deposition Author(s): Brodin, J.D., Smith, S.J., Tezcan, F.A.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-FG02-10ER46677

Revision History  

• Version 1.0: 2016-06-08
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary