1NP7 | pdb_00001np7

Crystal Structure Analysis of Synechocystis sp. PCC6803 cryptochrome

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.233 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 

Literature

Identification of a new cryptochrome class: structure, function, and evolution

Brudler, R., Hitomi, K., Daiyasu, H., Toh, H., Kucho, K., Ishiura, M., Kanehisa, M., Roberts, V.A., Todo, T., Tainer, J.A., Getzoff, E.D.

(2003) Mol Cell 11: 59-67

  • DOI: https://doi.org/10.1016/s1097-2765(03)00008-x
  • Primary Citation Related Structures: 
    1NP7

  • PubMed Abstract: 

    Cryptochrome flavoproteins, which share sequence homology with light-dependent DNA repair photolyases, function as photoreceptors in plants and circadian clock components in animals. Here, we coupled sequencing of an Arabidopsis cryptochrome gene with phylogenetic, structural, and functional analyses to identify a new cryptochrome class (cryptochrome DASH) in bacteria and plants, suggesting that cryptochromes evolved before the divergence of eukaryotes and prokaryotes. The cryptochrome crystallographic structure, reported here for Synechocystis cryptochrome DASH, reveals commonalities with photolyases in DNA binding and redox-dependent function, despite distinct active-site and interaction surface features. Whole genome transcriptional profiling together with experimental confirmation of DNA binding indicated that Synechocystis cryptochrome DASH functions as a transcriptional repressor.

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

Macromolecule Content 

  • Total Structure Weight: 116.08 kDa 
  • Atom Count: 8,467 
  • Modeled Residue Count: 966 
  • Deposited Residue Count: 978 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA photolyase
A, B
489Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
Find proteins for P77967 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P77967 
Go to UniProtKB:  P77967
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP77967
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.233 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.284α = 90
b = 89.477β = 120.46
c = 121.687γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-28
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description