1JMB

CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Toward the de novo design of a catalytically active helix bundle: a substrate-accessible carboxylate-bridged dinuclear metal center.

Di Costanzo, L.Wade, H.Geremia, S.Randaccio, L.Pavone, V.DeGrado, W.F.Lombardi, A.

(2001) J.Am.Chem.Soc. 123: 12749-12757

  • Primary Citation of Related Structures:  1JM0

  • PubMed Abstract: 
  • De novo design of proteins provides an attractive approach to uncover the essential features required for their functions. Previously, we described the design and crystal structure determination of a di-Zn(II) complex of "due-ferri-1" (DF1), a protei ...

    De novo design of proteins provides an attractive approach to uncover the essential features required for their functions. Previously, we described the design and crystal structure determination of a di-Zn(II) complex of "due-ferri-1" (DF1), a protein patterned after the diiron-dimanganese class of redox-active proteins [Lombardi, A.; Summa, C.; Geremia, S.; Randaccio, L.; Pavone, V.; DeGrado, W. F. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 6298-6305]. The overall structure of DF1, which contains a carboxylate-bridged dinuclear metal site, agrees well with the intended design. However, access to this dimetal site is blocked by a pair of hydrophobic leucine residues (L13 and L13'), which prevent facile entry of metal ions and small molecules. We have now taken the next step in the eventual construction of a catalytically active metalloenzyme by engineering an active site cavity into DF1 through the replacement of these two leucine residues with smaller residues. The crystal structure of the dimanganous form of L13A-DF1 indeed shows a substrate access channel to the dimetal center. In the crystal structure, water molecules and a ligating dimethyl sulfoxide molecule, which forms a monatomic bridge between the metal ions, occupy the cavity. Furthermore, the diferric form of a derivative of L13A-DF1, DF2, is shown to bind azide, acetate, and small aromatic molecules.


    Related Citations: 
    • Tertiary Templates for the Design of Diiron Proteins
      Summa, C.M.,Lombardi, A.,Lewis, M.,DeGrado, W.F.
      (1999) Curr.Opin.Struct.Biol. 9: 500
    • Retrostructural Analysis of Metalloproteins: Application to the Design of a Minimal Model for Diiron Proteins
      Lombardi, A.,Summa, C.M.,Geremia, S.,Randaccio, L.,Pavone, V.,DeGrado, W.F.
      (2000) Proc.Natl.Acad.Sci.USA 97: 6298
    • De Novo Design and Structural Characterization of Proteins and Metalloproteins
      DeGrado, W.F.,Summa, C.M.,Pavone, V.,Nastri, F.,Lombardi, A.
      (1999) Annu.Rev.Biochem. 68: 779


    Organizational Affiliation

    Biocrystallography Centre of Excellence, Department of Chemical Science, University of Trieste, Via L. Giorgieri 1, I-34127 Trieste, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (FOUR-HELIX BUNDLE MODEL)
A, B, C
50N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A, B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
A, B, C
NON-POLYMERH2 N

--

ACE
Query on ACE
A, B, C
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.247 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 37.121α = 90.00
b = 112.451β = 90.00
c = 79.877γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CCP4data scaling
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-01-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance