3NMK

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

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This is version 1.2 of the entry. See complete history. 


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
ZN
Query on ZN
Download Ideal Coordinates CCD File 
I [auth B],
J [auth C]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.467α = 90
b = 99.467β = 90
c = 109.544γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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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, Refinement description