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⇱ RCSB PDB - 1L2H: Crystal structure of Interleukin 1-beta F42W/W120F mutant

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Structures from the PDB archive		1,068,577
Computed Structure Models (CSM)

 1L2H | pdb_00001l2h

Crystal structure of Interleukin 1-beta F42W/W120F mutant

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 
    0.193 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.150 (DCC) 

wwPDB Validation  3D Report Full Report


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


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 Search on PubMed
  • DOI: https://doi.org/10.1107/s0907444902021704
  • Primary Citation 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.

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

Macromolecule Content 

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

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin 1-beta153Homo sapiensMutation(s): 2 
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UniProt & NIH Common Fund Data Resources
Find proteins for P01584 (Homo sapiens)
Explore P01584 
Go to UniProtKB:  P01584
PHAROS:  P01584
GTEx:  ENSG00000125538 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01584
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free:  0.193 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.150 (DCC) 
Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.89α = 90
b = 53.89β = 90
c = 77.36γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.