3NMJ | pdb_00003nmj

Crystal structure of a nickel mediated dimer for the phenanthroline-modified cytochrome cb562 variant, MBP-Phen2

• PDB DOI: https://doi.org/10.2210/pdb3NMJ/pdb

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


• Deposited: 2010-06-22 Released: 2010-11-24 
• Deposition Author(s): Radford, R.J., Tezcan, F.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.238 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

Porous protein frameworks with unsaturated metal centers in sterically encumbered coordination sites.

Radford, R.J., Lawrenz, M., Nguyen, P.C., McCammon, J.A., Tezcan, F.A.

(2011) Chem Commun (Camb) 47: 313-315

• PubMed: 20740227 
• DOI: https://doi.org/10.1039/c0cc02168g
• Primary Citation Related Structures: 
  3NMI, 3NMJ, 3NMK


• PubMed Abstract: 
  

  Described is an engineered metal-binding protein, MBPPhen2, which forms porous crystalline frameworks that feature coordinatively unsaturated Zn- and Ni-centers.

---

Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Dr, La Jolla, CA 92037, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.38 kDa 
• Atom Count: 3,437 
• Modeled Residue Count: 423 
• 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): 6  Gene Names: cybC
UniProt
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], G [auth B], K [auth C], M [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
PXX	F [auth A], H [auth B], L [auth C], N [auth D]	N-1,10-phenanthrolin-5-ylacetamide C14 H11 N3 O AAJXINSCZMZERD-UHFFFAOYSA-N
NI	I [auth B], J [auth C]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.238 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.291	α = 90
b = 99.291	β = 90
c = 109.317	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-24 
Deposition Author(s): Radford, R.J., Tezcan, F.A.

Revision History  

• Version 1.0: 2010-11-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations