3M15

A Zn-mediated asymmetric trimer of a cytochrome cb562 variant (D74A-RIDC1)

• PDB DOI: https://doi.org/10.2210/pdb3M15/pdb

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


• Deposited: 2010-03-04 Released: 2011-01-12 
• Deposition Author(s): Tezcan, F.A., Ni, T.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.313 
• R-Value Work: 0.220 
• R-Value Observed: 0.226 

Literature

Structural characterization of a microperoxidase inside a metal-directed protein cage.

Ni, T.W., Tezcan, F.A.

(2010) Angew Chem Int Ed Engl 49: 7014-7018

• PubMed: 20721993 
• DOI: https://doi.org/10.1002/anie.201001487
• Primary Citation of Related Structures:  
  3M15, 3M4B, 3M4C

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0356, La Jolla, CA 92093, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 36.95 kDa 
• Atom Count: 2,609 
• Modelled Residue Count: 318 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562	A, B, C	106	Escherichia coli	Mutation(s): 12  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	D [auth A], F [auth B], H [auth C]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
ZN	E [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.313 
• R-Value Work: 0.220 
• R-Value Observed: 0.226 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.879	α = 90
b = 74.819	β = 90
c = 81.358	γ = 90

Software Package:

Software Name	Purpose
SAINT	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
APEX	data collection
SAINT	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-12 
Deposition Author(s): Tezcan, F.A., Ni, T.W.

Revision History  

• Version 1.0: 2011-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-03-07
  Changes: Data collection
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-21
  Changes: Data collection, Refinement description