6KIJ

Crystal structure of yedK with ssDNA containing an abasic site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of yedK

Wang, N.Bao, H.Huang, H.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SOS response-associated protein
B
227Escherichia coliMutation(s): 0 
Gene Names: yedK
EC: 3.4.-.-
Find proteins for A0A2S5ZH06 (Escherichia coli)
Go to UniProtKB:  A0A2S5ZH06
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*TP*TP*CP*GP*TP*CP*G)-3')A9Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PED
Query on PED

Download SDF File 
Download CCD File 
B
PENTANE-3,4-DIOL-5-PHOSPHATE
OPEN FORM OF 1'-2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
C5 H13 O6 P
FQKLTSRHTQGSQZ-CRCLSJGQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.152 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.444α = 90.00
b = 44.080β = 102.33
c = 55.148γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-3000data reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2018YFC1004500
National Natural Science Foundation of ChinaChinathe Thousand Young Talents Program
National Natural Science Foundation of ChinaChina31800619

Revision History 

  • Version 1.0: 2019-08-07
    Type: Initial release