5ZCW

Structure of the Methanosarcina mazei class II CPD-photolyase in complex with intact, phosphodiester linked, CPD-lesion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Twist and turn: a revised structural view on the unpaired bubble of class II CPD photolyase in complex with damaged DNA

Maestre-Reyna, M.Yamamoto, J.Huang, W.C.Tsai, M.D.Essen, L.-O.Bessho, Y.

(2018) Iucrj 5: --


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deoxyribodipyrimidine photolyase
A, B
482Methanosarcina mazeiMutation(s): 1 
Find proteins for A0A0F8I5V2 (Methanosarcina mazei)
Go to UniProtKB:  A0A0F8I5V2
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*TP*CP*GP*GP*CP*(TTD)P*CP*GP*CP*GP*CP*AP*A)-3'C,E14synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*TP*GP*CP*GP*CP*GP*AP*AP*GP*CP*CP*GP*AP*T)-3'D,F14synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
FAD
Query on FAD

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A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TTD
Query on TTD
C, E
DNA LINKINGC20 H28 N4 O15 P2DT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.100α = 90.00
b = 114.420β = 90.00
c = 166.420γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-22
    Type: Initial release