1QOW | pdb_00001qow

Mersacidin from Bacillus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Work: 
    0.137 (DCC) 
  • R-Value Observed: 
    0.141 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1QOW

This is version 2.0 of the entry. See complete history

Literature

Ab initio structure determination of the lantibiotic mersacidin.

Schneider, T.R.Karcher, J.Pohl, E.Lubini, P.Sheldrick, G.M.

(2000) Acta Crystallogr D Biol Crystallogr 56: 705-713

  • DOI: https://doi.org/10.1107/s0907444900003711
  • Primary Citation Related Structures: 
    1QOW

  • PubMed Abstract: 

    The crystal structure of mersacidin, a potential novel antibiotic against methicillin- and vancomycin-resistant Staphylococcus aureus strains, has been determined by ab initio methods. Despite all crystals being merohedrally twinned, an accurate structural model with an R value of 13.4% has been obtained at atomic resolution. With six molecules in the asymmetric unit and no atom heavier than sulfur, the structure corresponds to a protein of 120 amino acids and is the largest approximately equal-atom unknown structure solved by direct methods. In the crystal, the molecule assumes a compact fold different from that found by NMR in solution. Comparison of the NCS-related molecules reveals regions of variable flexibility. The region highly homologous to the related antibiotic actagardine is very rigid and possibly defines an essential building block of this class of new antibacterial substances.


  • Organizational Affiliation
    • University of Göttingen, Department of Structural Chemistry, Germany. trs@shelx.uni-ac-gwdg.de

Macromolecule Content 

  • Total Structure Weight: 11.29 kDa 
  • Atom Count: 825 
  • Modeled Residue Count: 120 
  • Deposited Residue Count: 120 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MERSACIDIN
A, B, C, D, E
A, B, C, D, E, F
20Bacillus sp. (in: firmicutes)Mutation(s): 0 
UniProt
Find proteins for P43683 (Bacillus sp. (strain HIL-Y85/54728))
Explore P43683 
Go to UniProtKB:  P43683
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43683
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MOH

Query on MOH



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth B]
K [auth C]
G [auth A],
H [auth A],
I [auth A],
J [auth B],
K [auth C],
L [auth D],
M [auth E],
N [auth E],
O [auth F]
METHANOL
C H4 O
OKKJLVBELUTLKV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
DBB
Query on DBB
A, B, C, D, E
A, B, C, D, E, F
D-PEPTIDE LINKINGC4 H9 N O2

--

DHA
Query on DHA
A, B, C, D, E
A, B, C, D, E, F
PEPTIDE LINKINGC3 H5 N O2SER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Work:  0.137 (DCC) 
  • R-Value Observed: 0.141 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.09α = 90
b = 46.09β = 90
c = 31.02γ = 120
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
  • Version 1.2: 2011-07-27
    Changes: Atomic model, Data collection, Derived calculations, Other, Refinement description
  • Version 1.3: 2012-11-30
    Changes: Other
  • Version 1.4: 2019-04-17
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.5: 2019-05-22
    Changes: Data collection, Refinement description
  • Version 1.6: 2019-07-24
    Changes: Data collection, Experimental preparation
  • Version 1.7: 2019-10-09
    Changes: Data collection, Database references, Other
  • Version 2.0: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Polymer sequence