Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 116.08 kDa 
• Atom Count: 8467 
• Modelled Residue Count: 966 
• Deposited Residue Count: 978 
• Unique protein chains: 1

1NP7

Crystal Structure Analysis of Synechocystis sp. PCC6803 cryptochrome

• DOI: 10.2210/pdb1NP7/pdb

• Classification: LYASE
• Organism(s): Synechocystis sp. PCC 6803
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-01-17 Released: 2003-01-28 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.233 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 

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

• PubMed: 12535521 
• DOI: 10.1016/s1097-2765(03)00008-x
• Primary Citation of 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA photolyase	A, B	489	Synechocystis sp. PCC 6803	Mutation(s): 0
Find proteins for P77967 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P77967  Go to UniProtKB:  P77967

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A], G [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
SO4	C [auth A], D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.233 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.284	α = 90
b = 89.477	β = 120.46
c = 121.687	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-01-17 
• Released Date: 2003-01-28 
Deposition Author(s): 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.

Revision History  

• 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