3SHI

Crystal structure of human MMP1 catalytic domain at 2.2 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.209 

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

  • 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 ...

    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.Mol.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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Interstitial collagenase
A, G, M
156Homo sapiensMutation(s): 0 
Gene Names: MMP1 (CLG)
EC: 3.4.24.7
Find proteins for P03956 (Homo sapiens)
Go to Gene View: MMP1
Go to UniProtKB:  P03956
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, G, M
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, G, M
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 147.694α = 90.00
b = 54.528β = 120.69
c = 94.905γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALAdata scaling
CrysalisProdata collection
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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