3NMJ

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

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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

  • DOI: https://doi.org/10.1039/c0cc02168g
  • Primary Citation of 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.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562
A, B, C, D
106Escherichia coliMutation(s): 6 
Gene Names: cybC
UniProt
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABE7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download Ideal Coordinates CCD File 
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
Query on PXX
Download Ideal Coordinates CCD File 
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
Query on NI
Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.291α = 90
b = 99.291β = 90
c = 109.317γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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