3SHI

Crystal structure of human MMP1 catalytic domain at 2.2 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The catalytic domain of MMP-1 studied through tagged lanthanides.

Bertini, I.Calderone, V.Cerofolini, L.Fragai, M.Geraldes, C.F.Hermann, P.Luchinat, C.Parigi, G.Teixeira, J.M.

(2012) FEBS Lett 586: 557-567

  • DOI: 10.1016/j.febslet.2011.09.020
  • Primary Citation of Related Structures:  
    3SHI

  • PubMed Abstract: 
  • Pseudocontact shifts (pcs) and paramagnetic residual dipolar couplings (rdc) provide structural information that can be used to assess the adequacy of a crystallographic structure to represent the solution structure of a protein. This can be done by attaching a lanthanide binding tag to the protein ...

    Pseudocontact shifts (pcs) and paramagnetic residual dipolar couplings (rdc) provide structural information that can be used to assess the adequacy of a crystallographic structure to represent the solution structure of a protein. This can be done by attaching a lanthanide binding tag to the protein. There are cases in which only local rearrangements are sufficient to match the NMR data and cases where significant secondary structure or domain rearrangements from the solid state to the solution state are needed. We show that the two cases are easily distinguishable. Whereas the use of solution restraints in the latter case is described in the literature, here we deal with how to obtain a better model of the solution structure in a case (the catalytic domain of the matrix metalloproteinase MMP-1) of the former class.


    Related Citations: 
    • Crystal structures of recombinant 19-kDa human fibroblast collagenase complexed to itself.
      Lovejoy, B., Hassell, A.M., Luther, M.A., Weigl, D., Jordan, S.R.
      (1994) Biochemistry 33: 8207
    • 1.56 A structure of mature truncated human fibroblast collagenase.
      Spurlino, J.C., Smallwood, A.M., Carlton, D.D., Banks, T.M., Vavra, K.J., Johnson, J.S., Cook, E.R., Falvo, J., Wahl, R.C., Pulvino, T.A.
      (1994) Proteins 19: 98
    • Crystal structures of MMP-1 and -13 reveal the structural basis for selectivity of collagenase inhibitors.
      Lovejoy, B., Welch, A.R., Carr, S., Luong, C., Broka, C., Hendricks, R.T., Campbell, J.A., Walker, K.A., Martin, R., Van Wart, H., Browner, M.F.
      (1999) Nat Struct Biol 6: 217

    Organizational Affiliation

    Magnetic Resonance Center (CERM), University of Florence, via Sacconi 6, 50019 Sesto Fiorentino, Italy. ivanobertini@cerm.unifi.it



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interstitial collagenase AGM156Homo sapiensMutation(s): 0 
Gene Names: MMP1CLG
EC: 3.4.24.7
Find proteins for P03956 (Homo sapiens)
Explore P03956 
Go to UniProtKB:  P03956
NIH Common Fund Data Resources
PHAROS:  P03956
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.694α = 90
b = 54.528β = 120.69
c = 94.905γ = 90
Software Package:
Software NamePurpose
CrysalisProdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2011-10-12
    Changes: Database references
  • Version 1.2: 2012-03-21
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description