6O4M

Racemic melittin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Retention of Native Quaternary Structure in Racemic Melittin Crystals.

Kurgan, K.W.Kleman, A.F.Bingman, C.A.Kreitler, D.F.Weisblum, B.Forest, K.T.Gellman, S.H.

(2019) J.Am.Chem.Soc. 141: 7704-7708

  • DOI: 10.1021/jacs.9b02691

  • PubMed Abstract: 
  • Racemic crystallography has been used to elucidate the secondary and tertiary structures of peptides and small proteins that are recalcitrant to conventional crystallization. It is unclear, however, whether racemic crystallography can capture native ...

    Racemic crystallography has been used to elucidate the secondary and tertiary structures of peptides and small proteins that are recalcitrant to conventional crystallization. It is unclear, however, whether racemic crystallography can capture native quaternary structure, which could be disrupted by heterochiral associations. We are exploring the use of racemic crystallography to characterize the self-assembly behavior of membrane-associated peptides, very few of which have been crystallized. We report a racemic crystal structure of the membrane-active peptide melittin; the new structure allows comparison with a previously reported crystal structure of L-melittin. The tetrameric assembly observed in crystalline L-melittin has been proposed to represent the tetrameric state detected in solution for this peptide. This tetrameric assembly is precisely reproduced in the racemic crystal, which strengthens the conclusion that the tetramer is biologically relevant. More broadly, these findings suggest that racemic crystallography can provide insight on native quaternary structure.


    Organizational Affiliation

    Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences , University at Buffalo , Buffalo , New York 14203-1102 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-Melittin
D, C
27Apis melliferaMutation(s): 0 
Gene Names: MELT
Find proteins for P01501 (Apis mellifera)
Go to UniProtKB:  P01501
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Melittin
A, B
27Apis melliferaMutation(s): 0 
Gene Names: MELT
Find proteins for P01501 (Apis mellifera)
Go to UniProtKB:  P01501
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  12 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
A, B, C, D
NON-POLYMERH2 N

--

DIL
Query on DIL
C, D
D-PEPTIDE LINKINGC6 H13 N O2

--

DPR
Query on DPR
C, D
D-PEPTIDE LINKINGC5 H9 N O2

--

DLY
Query on DLY
C, D
D-PEPTIDE LINKINGC6 H14 N2 O2

--

DSN
Query on DSN
C, D
D-PEPTIDE LINKINGC3 H7 N O3

--

DVA
Query on DVA
C, D
D-PEPTIDE LINKINGC5 H11 N O2

--

DTH
Query on DTH
C, D
D-PEPTIDE LINKINGC4 H9 N O3

--

DLE
Query on DLE
C, D
D-PEPTIDE LINKINGC6 H13 N O2

--

DAL
Query on DAL
C, D
D-PEPTIDE LINKINGC3 H7 N O2

--

DGN
Query on DGN
C, D
D-PEPTIDE LINKINGC5 H10 N2 O3

--

DTR
Query on DTR
C, D
D-PEPTIDE LINKINGC11 H12 N2 O2

--

DAR
Query on DAR
C, D
D-PEPTIDE LINKINGC6 H15 N4 O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 38.380α = 90.00
b = 58.990β = 110.60
c = 44.020γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01GM061238

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-05-29
    Type: Data collection, Database references
  • Version 1.2: 2019-12-18
    Type: Author supporting evidence