1LJ7

Crystal structure of calcium-depleted human C-reactive protein from perfectly twinned data


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.186 

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This is version 1.4 of the entry. See complete history


Literature

The three-dimensional structure of calcium-depleted human C-reactive protein from perfectly twinned crystals.

Ramadan, M.A.Shrive, A.K.Holden, D.Myles, D.A.Volanakis, J.E.DeLucas, L.J.Greenhough, T.J.

(2002) Acta Crystallogr D Biol Crystallogr 58: 992-1001

  • DOI: https://doi.org/10.1107/s0907444902005693
  • Primary Citation of Related Structures:  
    1LJ7

  • PubMed Abstract: 

    C-reactive protein is a member of the pentraxin family of oligomeric serum proteins which has been conserved through evolution, homologues having been found in every species in which they have been sought. Human C-reactive protein (hCRP) is the classical acute-phase reactant produced in large amounts in response to tissue damage and inflammation and is used almost universally as a clinical indicator of infection and inflammation. The role of hCRP in host defence and the calcium-dependent ligand-binding specificity of hCRP for phosphocholine moieties have long been recognized. In order to clarify the structural rearrangements associated with calcium binding, the reported affinity of calcium-depleted hCRP for polycations and other ligands, and the role of calcium in protection against denaturation and proteolysis, the structure of calcium-depleted hCRP has been determined by X-ray crystallography. Crystals of calcium-depleted hCRP are invariably twinned and those suitable for analysis are merohedral type II twins of point group 4 single crystals. The structure has been solved by molecular replacement using the calcium-bound hCRP structure [Shrive et al. (1996), Nature Struct. Biol. 3, 346-354]. It reveals two independent pentamers which form a face-to-face decamer across a dyad near-parallel to the twinning twofold axis. Cycles of intensity deconvolution, density modification (tenfold NCS) and model building, eventually including refinement, give a final R factor of 0.19 (R(free) = 0.20). Despite poor definition in some areas arising from the limited resolution of the data and from the twinning and disorder, the structure reveals the probable mode of twinning and the conformational changes, localized in one of the calcium-binding loops, which accompany calcium binding.


  • Organizational Affiliation

    School of Life Sciences, Keele University, Staffordshire ST5 5BG, England.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-reactive protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
206Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02741 (Homo sapiens)
Explore P02741 
Go to UniProtKB:  P02741
PHAROS:  P02741
GTEx:  ENSG00000132693 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02741
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.186 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.31α = 90
b = 102.31β = 90
c = 309.23γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
ROTAVATAdata reduction
CCP4model building
X-PLORrefinement
CCP4data scaling
ROTAVATAdata scaling
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-05
    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: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Refinement description