2QLA | pdb_00002qla

Crystal Structure of a 16-Helix Bundle Architecture Produced by the Zinc-Mediated Self Assembly of Four Cytochrome cb562 Molecules

• PDB DOI: https://doi.org/10.2210/pdb2QLA/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-07-12 Released: 2007-11-06 
• Deposition Author(s): Tezcan, F.A., Salgado, E.N., Faraone-Mennella, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.295 (Depositor), 0.298 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Model: experimental

Literature

Controlling protein-protein interactions through metal coordination: assembly of a 16-helix bundle protein.

Salgado, E.N., Faraone-Mennella, J., Tezcan, F.A.

(2007) J Am Chem Soc 129: 13374-13375

• PubMed: 17929927 
• DOI: https://doi.org/10.1021/ja075261o
• Primary Citation Related Structures: 
  2QLA

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

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: 49.63 kDa 
• Atom Count: 3,483 
• Modeled Residue Count: 424 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562	A, B, C, D	106	Escherichia coli	Mutation(s): 5  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	E [auth A], G [auth B], I [auth C], K [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
ZN	F [auth A], H [auth B], J [auth C], L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.295 (Depositor), 0.298 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.984	α = 90
b = 66.659	β = 90
c = 68.901	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
APEX	data collection
SAINT	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-06 
Deposition Author(s): Tezcan, F.A., Salgado, E.N., Faraone-Mennella, J.

Revision History  

• Version 1.0: 2007-11-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-18
  Changes: Advisory, Refinement description
• Version 1.3: 2018-03-07
  Changes: Data collection
• Version 1.4: 2021-10-20
  Changes: Advisory, Database references, Derived calculations
• Version 1.5: 2023-08-30
  Changes: Data collection, Refinement description