3FOO

A Triangular Cytochrome b562 Superstructure Mediated by Ni Coordination - Monoclinic Form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.213 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

A superprotein triangle driven by nickel(II) coordination: exploiting non-natural metal ligands in protein self-assembly

Radford, R.J.Tezcan, F.A.

(2009) J Am Chem Soc 131: 9136-9137

  • DOI: https://doi.org/10.1021/ja9000695
  • Primary Citation of Related Structures:  
    3FOO, 3FOP

  • PubMed Abstract: 

    We previously devised a strategy (metal-directed protein self-assembly, MDPSA) that utilizes the simultaneous stability, lability, and directionality of metal-ligand bonds to drive protein-protein interactions. Here we show that both the structural and functional scopes of MDPSA can be broadened by incorporation of non-natural metal-chelating ligands onto protein surfaces. A cytochrome cb(562) variant, MBP-Phen1, which features a covalently attached phenanthroline (Phen) group on its surface, self-assembles into an unusual triangular architecture (Ni(3):MBP-Phen1(3)) upon binding Ni as a result of specific Phen-protein interactions. The crystal structure of Ni(3):MBP-Phen1(3) reveals that the Phen group is buried in a small pocket on the protein surface, which results in an unsaturated Ni coordination environment.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
106Escherichia coliMutation(s): 7 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
AB [auth K]
CA [auth E]
EB [auth L]
GA [auth F]
KA [auth G]
AB [auth K],
CA [auth E],
EB [auth L],
GA [auth F],
KA [auth G],
M [auth A],
OA [auth H],
Q [auth B],
SA [auth I],
U [auth C],
WA [auth J],
Y [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
PXX
Query on PXX

Download Ideal Coordinates CCD File 
BB [auth K]
DA [auth E]
FB [auth L]
HA [auth F]
LA [auth G]
BB [auth K],
DA [auth E],
FB [auth L],
HA [auth F],
LA [auth G],
N [auth A],
PA [auth H],
R [auth B],
TA [auth I],
V [auth C],
XA [auth J],
Z [auth D]
N-1,10-phenanthrolin-5-ylacetamide
C14 H11 N3 O
AAJXINSCZMZERD-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CB [auth K]
DB [auth K]
EA [auth E]
AA [auth D],
BA [auth D],
CB [auth K],
DB [auth K],
EA [auth E],
FA [auth E],
GB [auth L],
HB [auth L],
IA [auth F],
JA [auth F],
MA [auth G],
NA [auth G],
O [auth A],
P [auth A],
QA [auth H],
RA [auth H],
S [auth B],
T [auth B],
UA [auth I],
VA [auth I],
W [auth C],
X [auth C],
YA [auth J],
ZA [auth J]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.339α = 90
b = 107.396β = 105.52
c = 102.051γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description