1QNF

STRUCTURE OF PHOTOLYASE

• PDB DOI: https://doi.org/10.2210/pdb1QNF/pdb

• Classification: DNA REPAIR
• Organism(s): Synechococcus elongatus PCC 6301
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 1997-07-04 Released: 1998-01-14 
• Deposition Author(s): Miki, K., Kitadokoro, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.239 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 

Literature

Crystal structure of DNA photolyase from Anacystis nidulans

Tamada, T., Kitadokoro, K., Higuchi, Y., Inaka, K., Yasui, A., de Ruiter, P.E., Eker, A.P., Miki, K.

(1997) Nat Struct Biol 4: 887-891

• PubMed: 9360600 
• DOI: https://doi.org/10.1038/nsb1197-887
• Primary Citation of Related Structures:  
  1QNF


• PubMed Abstract: 
  

  The crystal structure at 1.8 A resolution of 8-HDF type photolyase from A. nidulans shows a backbone structure similar to that of MTHF type E. coli photolyase but reveals a completely different binding site for the light-harvesting cofactor.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 55.68 kDa 
• Atom Count: 4,029 
• Modelled Residue Count: 475 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOLYASE	A	484	Synechococcus elongatus PCC 6301	Mutation(s): 0  EC: 4.1.99.3
UniProt
Find proteins for P05327 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1)) Explore P05327  Go to UniProtKB:  P05327

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
HDF	C [auth A]	8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)-5-DEAZAISOALLOXAZINE C16 H17 N3 O7 AUEILLWDYUBWCM-AGIUHOORSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.239 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.17	α = 90
b = 91.17	β = 90
c = 135.54	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-01-14 
Deposition Author(s): Miki, K., Kitadokoro, K.

Revision History  

• Version 1.0: 1998-01-14
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Other