1H34

Crystal structure of lima bean trypsin inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.275 
  • R-Value Observed: 0.253 

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This is version 1.4 of the entry. See complete history. 


Literature

In-House Phase Determination of the Lima Bean Trypsin Inhibitor: A Low-Resolution Sulfur-Sad Case

Debreczeni, J.E., Bunkoczi, G., Girmann, B., Sheldrick, G.M.

(2003) Acta Crystallogr D Biol Crystallogr 59: 393

  • DOI: 10.1107/s0907444902020917
  • Primary Citation of Related Structures:  
    1H34

  • PubMed Abstract: 

    • SAD (single-wavelength anomalous diffraction) has enormous potential for phasing proteins using only the anomalous signal of the almost ubiquitous native sulfur, but requires extremely precise data. The previously unknown structure of the lima bean trypsin inhibitor (LBTI) was solved using highly redundant data collected to 3 A using a CCD detector with a rotating-anode generator and three-circle goniometer ...

    SAD (single-wavelength anomalous diffraction) has enormous potential for phasing proteins using only the anomalous signal of the almost ubiquitous native sulfur, but requires extremely precise data. The previously unknown structure of the lima bean trypsin inhibitor (LBTI) was solved using highly redundant data collected to 3 A using a CCD detector with a rotating-anode generator and three-circle goniometer. The seven 'super-S' atoms (disulfide bridges) were located by dual-space recycling with SHELXD and the high solvent content enabled the density-modification program SHELXE to generate high-quality maps despite the modest resolution. Subsequently, a 2.05 A synchrotron data set was collected and used for further phase extension and structure refinement.

    Organizational Affiliation: 

    Lehrstuhl für Strukturchemie, Georg-August Universität, Göttingen, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BOWMAN-BIRK TYPE PROTEINASE INHIBITORA83Phaseolus lunatusMutation(s): 0 
UniProt
Find proteins for P01056 (Phaseolus lunatus)
Explore P01056 
Go to UniProtKB:  P01056
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01056
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.275 
  • R-Value Observed: 0.253 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.157α = 90
b = 109.157β = 90
c = 109.157γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHELXEphasing
SHELXL-97refinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-22
    Changes: Data collection, Other, Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection