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Time-resolved SFX structure of the class II photolyase complexed with a thymine dimer (1 nanosecond pump-probe delay)

X-ray diffraction
2.27Å resolution
PDB entry 8oy5 coloured by chain, front view.
PDB entry 8oy5 coloured by chain, side view.
PDB entry 8oy5 coloured by chain, top view.
Source organisms:
Assembly composition:
hetero trimer (preferred)
Entry contents: 1 distinct polypeptide molecule
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Deoxyribodipyrimidine photo-lyase and DNA
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Multimeric state: hetero trimer
Accessible surface area: 21947.84 Å2
Buried surface area: 5528.04 Å2
Dissociation area: 2,050.9 Å2
Dissociation energy (ΔGdiss): 4.99 kcal/mol
Dissociation entropy (TΔSdiss): 21.52 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-235648
Assembly 2
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Assembly Name: Deoxyribodipyrimidine photo-lyase and DNA
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Multimeric state: hetero trimer
Accessible surface area: 20782.48 Å2
Buried surface area: 5111.69 Å2
Dissociation area: 1,959.75 Å2
Dissociation energy (ΔGdiss): 6.24 kcal/mol
Dissociation entropy (TΔSdiss): 20.98 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-235648

Macromolecules

Deoxyribodipyrimidine photo-lyase
Chains: A, B
Length: 498 amino acids
Theoretical weight: 57.04 KDa
Source organism: Methanosarcina mazei Go1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8PYK9 (Residues: 1-464; Coverage: 100%)
Gene name: MM_0852
Pfam: DNA photolyase
Deoxyribodipyrimidine photo-lyase in PDB entry 8oy5, assembly 1, front view.
Deoxyribodipyrimidine photo-lyase in PDB entry 8oy5, assembly 1, side view.
Deoxyribodipyrimidine photo-lyase in PDB entry 8oy5, assembly 1, top view.
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DNA chains C, E
Name: CPD-COMPRISING OLIGONUCLEOTIDE
Representative chains: C, E
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 13 nucleotides
Theoretical weight: 4.26 KDa
CPD-COMPRISING OLIGONUCLEOTIDE in PDB entry 8oy5, assembly 1, front view.
CPD-COMPRISING OLIGONUCLEOTIDE in PDB entry 8oy5, assembly 1, side view.
CPD-COMPRISING OLIGONUCLEOTIDE in PDB entry 8oy5, assembly 1, top view.
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DNA chains D, F
Name: COUNTERSTRAND-OLIGONUCLEOTIDE
Representative chains: D, F
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 14 nucleotides
Theoretical weight: 4.31 KDa
COUNTERSTRAND-OLIGONUCLEOTIDE in PDB entry 8oy5, assembly 1, front view.
COUNTERSTRAND-OLIGONUCLEOTIDE in PDB entry 8oy5, assembly 1, side view.
COUNTERSTRAND-OLIGONUCLEOTIDE in PDB entry 8oy5, assembly 1, top view.
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