1H34 | pdb_00001h34

Crystal structure of lima bean trypsin inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1H34/pdb

• Classification: INHIBITOR
• Organism(s): Phaseolus lunatus
• Mutation(s): No 


• Deposited: 2002-08-21 Released: 2003-02-06 
• Deposition Author(s): Debreczeni, J.E., Bunkoczi, G., Girmann, B., Sheldrick, G.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.275 (Depositor) 
• R-Value Work: 
  0.220 (DCC) 
• R-Value Observed: 
  0.253 (Depositor) 

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

• PubMed: 12554963 
• DOI: https://doi.org/10.1107/s0907444902020917
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Lehrstuhl für Strukturchemie, Georg-August Universität, Göttingen, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 9.04 kDa 
• Atom Count: 502 
• Modeled Residue Count: 57 
• Deposited Residue Count: 83 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BOWMAN-BIRK TYPE PROTEINASE INHIBITOR	A	83	Phaseolus lunatus	Mutation(s): 0
UniProt
Find proteins for P01056 (Phaseolus lunatus) Explore P01056  Go to UniProtKB:  P01056

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.275 (Depositor) 
• R-Value Work:  0.220 (DCC) 
• R-Value Observed: 0.253 (Depositor) 

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.157	α = 90
b = 109.157	β = 90
c = 109.157	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing
SHELXE	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-02-06 
Deposition Author(s): Debreczeni, J.E., Bunkoczi, G., Girmann, B., Sheldrick, G.M.

Revision History  

• 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
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Other, Structure summary