3SJ1

PpcA M58D mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Pitfalls in the interpretation of structural changes in mutant proteins from crystal structures.

Pokkuluri, P.R.Yang, X.Londer, Y.Y.Schiffer, M.

(2012) J Struct Funct Genomics 13: 227-232

  • DOI: 10.1007/s10969-012-9147-1
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • PpcA is a small protein with 71 residues that contains three covalently bound hemes. The structures of single mutants at residue 58 have shown larger deviations in another part of the protein molecule than at the site of the mutation. Closer examinat ...

    PpcA is a small protein with 71 residues that contains three covalently bound hemes. The structures of single mutants at residue 58 have shown larger deviations in another part of the protein molecule than at the site of the mutation. Closer examination of the crystal packing has revealed the origin of this unexpected structural change. The site of mutation is within Van der Waals distance from another protein molecule related by a crystallographic twofold axis within the crystal. The structural changes occurred at or near the mutation site have led to a slight adjustment of the surface residues in contact. The observed deviations between the native and the mutant molecular structures are derived from the new crystal packing even though the two crystals are essentially isomorphous. Without careful consideration of the crystal lattice a non-expert looking at only the coordinates deposited in the Protein Data Bank could draw erroneous conclusion that mutation in one part of the molecule affected the structure of the protein in a distant part of the molecule.


    Organizational Affiliation

    Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C7X71Geobacter sulfurreducensMutation(s): 1 
Gene Names: ppcAGSU0612RW64_12645YM18_0596
Find proteins for Q8GGK7 (Geobacter sulfurreducens)
Explore Q8GGK7 
Go to UniProtKB:  Q8GGK7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
X
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
DXC
Query on DXC

Download CCD File 
X
(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
C24 H40 O4
KXGVEGMKQFWNSR-LLQZFEROSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
X
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.492α = 90
b = 32.492β = 90
c = 176.956γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-04
    Type: Initial release
  • Version 1.1: 2012-12-19
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Advisory, Data collection, Derived calculations, Refinement description