1YTT

YB SUBSTITUTED SUBTILISIN FRAGMENT OF MANNOSE BINDING PROTEIN-A (SUB-MBP-A), MAD STRUCTURE AT 110K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Direct observation of protein solvation and discrete disorder with experimental crystallographic phases.

Burling, F.T.Weis, W.I.Flaherty, K.M.Brunger, A.T.

(1996) Science 271: 72-77

  • DOI: 10.1126/science.271.5245.72
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A complete and accurate set of experimental crystallographic phases to a resolution of 1.8 angstroms was obtained for a 230-residue dimeric fragment of rat mannose-binding protein A with the use of multiwavelength anomalous dispersion (MAD) phasing. ...

    A complete and accurate set of experimental crystallographic phases to a resolution of 1.8 angstroms was obtained for a 230-residue dimeric fragment of rat mannose-binding protein A with the use of multiwavelength anomalous dispersion (MAD) phasing. An accurate image of the crystal structure could thus be obtained without resort to phases calculated from a model. Partially reduced disulfide bonds, local disorder, and differences in the mobility of chemically equivalent molecules are apparent in the experimental electron density map. A solvation layer is visible that includes well-ordered sites of hydration around polar and charged protein atoms, as well as diffuse, partially disordered solvent shells around exposed hydrophobic groups. Because the experimental phases and the resulting electron density map are free from the influence of a model, they provide a stringent test of theoretical models of macromolecular solvation, motion, and conformational heterogeneity.


    Related Citations: 
    • Physical Characterization and Crystallization of the Carbohydrate-Recognition Domain of a Mannose-Binding Protein from Rat
      Weis, W.I., Crichlow, G.V., Murthy, H.M., Hendrickson, W.A., Drickamer, K.
      (1991) J Biol Chem 266: 20678
    • Structure of the Calcium-Dependent Lectin Domain from a Rat Mannose-Binding Protein Determined by MAD Phasing
      Weis, W.I., Kahn, R., Fourme, R., Drickamer, K., Hendrickson, W.A.
      (1991) Science 254: 1608

    Organizational Affiliation

    Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MANNOSE-BINDING PROTEIN A
A, B
115Rattus norvegicusMutation(s): 0 
Gene Names: Mbl1
Find proteins for P19999 (Rattus norvegicus)
Go to UniProtKB:  P19999
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YB
Query on YB

Download CCD File 
A, B
YTTERBIUM (III) ION
Yb
AWSFICBXMUKWSK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.508α = 90
b = 72.216β = 90
c = 45.035γ = 90
Software Package:
Software NamePurpose
DENZO-SCALEPACKdata collection
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-06-10
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Derived calculations, Other