1L2H

Crystal structure of Interleukin 1-beta F42W/W120F mutant

• PDB DOI: https://doi.org/10.2210/pdb1L2H/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-02-21 Released: 2003-02-04 
• Deposition Author(s): Rudolph, M.G., Kelker, M.S., Schneider, T.R., Yeates, T.O., Oseroff, V., Heidary, D.K., Jennings, P.A., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.193 
• R-Value Work: 0.154 

Literature

Use of multiple anomalous dispersion to phase highly merohedrally twinned crystals of interleukin-1beta.

Rudolph, M.G., Kelker, M.S., Schneider, T.R., Yeates, T.O., Oseroff, V., Heidary, D.K., Jennings, P.A., Wilson, I.A.

(2003) Acta Crystallogr D Biol Crystallogr 59: 290-298

• PubMed: 12554939 
• DOI: https://doi.org/10.1107/s0907444902021704
• Primary Citation of Related Structures:  
  1L2H


• PubMed Abstract: 
  

  The crystal structure at 1.54 A resolution of a double mutant of interleukin-1beta (F42W/W120F), a cytokine secreted by macrophages, was determined by multiple-wavelength anomalous dispersion (MAD) using data from highly twinned selenomethionine-modified crystals. The space group is P4(3), with unit-cell parameters a = b = 53.9, c = 77.4 A. Self-rotation function analysis and various intensity statistics revealed the presence of merohedral twinning in crystals of both the native (twinning fraction alpha approximately 0.35) and SeMet (alpha approximately 0.40) forms. Structure determination and refinement are discussed with emphasis on the possible reasons for successful phasing using untreated twinned MAD data.

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Organizational Affiliation: 

Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.4 kDa 
• Atom Count: 1,294 
• Modelled Residue Count: 144 
• Deposited Residue Count: 153 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin 1-beta	A	153	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for P01584 (Homo sapiens) Explore P01584  Go to UniProtKB:  P01584
PHAROS:  P01584 GTEx:  ENSG00000125538

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.193 
• R-Value Work: 0.154 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.89	α = 90
b = 53.89	β = 90
c = 77.36	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-02-04 
Deposition Author(s): Rudolph, M.G., Kelker, M.S., Schneider, T.R., Yeates, T.O., Oseroff, V., Heidary, D.K., Jennings, P.A., Wilson, I.A.

Revision History  

• Version 1.0: 2003-02-04
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references
• Version 1.4: 2024-02-14
  Changes: Data collection