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Structure paper

TitleHoming endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s
Journal, issue, pagesTo Be Published
Publish dateJan 13, 2024 (structure data deposition date)
AuthorsChang, C. / Gao, Y.
External linksSearch PubMed
MethodsX-ray diffraction
Resolution1.42 - 2.11 Å
Structure data

PDB-8vmo:
Homing endonuclease I-PpoI-DNA complex:ground state at pH7.0 (K+ MES) with Na+
Method: X-RAY DIFFRACTION / Resolution: 1.68 Å

PDB-8vmp:
Homing endonuclease I-PpoI-DNA complex:reaction at pH7.0 (K+ MES) with 500 uM Mg2+ for 10s
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-8vmq:
Homing endonuclease I-PpoI-DNA complex:reaction at pH7.0 (K+ MES) with 500 uM Mg2+ for 20s
Method: X-RAY DIFFRACTION / Resolution: 1.48 Å

PDB-8vmr:
Homing endonuclease I-PpoI-DNA complex:reaction at pH7.0 (K+ MES) with 500 uM Mg2+ for 40s
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-8vms:
Homing endonuclease I-PpoI-DNA complex:reaction at pH7.0 (K+ MES) with 500 uM Mg2+ for 80s
Method: X-RAY DIFFRACTION / Resolution: 1.42 Å

PDB-8vmt:
Homing endonuclease I-PpoI-DNA complex:reaction at pH7.0 (K+ MES) with 500 uM Mg2+ for 160s
Method: X-RAY DIFFRACTION / Resolution: 1.48 Å

PDB-8vmu:
Homing endonuclease I-PpoI-DNA complex:reaction at pH7.0 (K+ MES) with 500 uM Mg2+ for 320s
Method: X-RAY DIFFRACTION / Resolution: 1.52 Å

PDB-8vmv:
Homing endonuclease I-PpoI-DNA complex:reaction at pH7.0 (K+ MES) with 500 uM Mg2+ for 600s
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

PDB-8vmw:
Homing endonuclease I-PpoI-DNA complex:ground state at pH6.0 (K+ MES) with Na+
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-8vmx:
Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mg2+ for 10s
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-8vmy:
Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mg2+ for 20s
Method: X-RAY DIFFRACTION / Resolution: 1.53 Å

PDB-8vmz:
Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mg2+ for 40s
Method: X-RAY DIFFRACTION / Resolution: 1.57 Å

PDB-8vn0:
Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mg2+ for 80s
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-8vn1:
Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mg2+ for 160s
Method: X-RAY DIFFRACTION / Resolution: 1.79 Å

PDB-8vn2:
Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mg2+ for 320s
Method: X-RAY DIFFRACTION / Resolution: 1.63 Å

PDB-8vn3:
Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mg2+ for 600s
Method: X-RAY DIFFRACTION / Resolution: 1.63 Å

PDB-8vn4:
Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mg2+ for 1200s
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-8vn5:
Homing endonuclease I-PpoI-DNA complex:ground state at pH8.0 (Tris) with Na+
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-8vn6:
Homing endonuclease I-PpoI-DNA complex:reaction at pH8.0 (Tris) with 500 uM Mg2+ for 10s
Method: X-RAY DIFFRACTION / Resolution: 1.54 Å

PDB-8vn7:
Homing endonuclease I-PpoI-DNA complex:reaction at pH8.0 (Tris) with 500 uM Mg2+ for 20s
Method: X-RAY DIFFRACTION / Resolution: 1.67 Å

PDB-8vn8:
Homing endonuclease I-PpoI-DNA complex:reaction at pH8.0 (Tris) with 500 uM Mg2+ for 40s
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-8vn9:
Homing endonuclease I-PpoI-DNA complex:reaction at pH8.0 (Tris) with 500 uM Mg2+ for 80s
Method: X-RAY DIFFRACTION / Resolution: 1.69 Å

PDB-8vna:
Homing endonuclease I-PpoI-DNA complex:reaction at pH8.0 (Tris) with 500 uM Mg2+ for 160s
Method: X-RAY DIFFRACTION / Resolution: 1.54 Å

PDB-8vnb:
Homing endonuclease I-PpoI-DNA complex:reaction at pH8.0 (Tris) with 500 uM Mg2+ for 240s
Method: X-RAY DIFFRACTION / Resolution: 1.72 Å

PDB-8vnc:
Homing endonuclease I-PpoI-DNA complex:reaction at pH8.0 (Tris) with 500 uM Mg2+ for 320s
Method: X-RAY DIFFRACTION / Resolution: 1.62 Å

PDB-8vnd:
Homing endonuclease I-PpoI-DNA complex:reaction at pH8.0 (Tris) with 500 uM Mg2+ for 600s
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-8vne:
Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 10s
Method: X-RAY DIFFRACTION / Resolution: 1.57 Å

PDB-8vnf:
Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 20s
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-8vng:
Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 40s
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-8vnh:
Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 80s
Method: X-RAY DIFFRACTION / Resolution: 1.76 Å

PDB-8vnj:
Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 120s
Method: X-RAY DIFFRACTION / Resolution: 1.61 Å

PDB-8vnk:
Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 160s
Method: X-RAY DIFFRACTION / Resolution: 1.61 Å

PDB-8vnl:
Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 240s
Method: X-RAY DIFFRACTION / Resolution: 1.64 Å

PDB-8vnm:
Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 320s
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

PDB-8vnn:
Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 480s
Method: X-RAY DIFFRACTION / Resolution: 1.79 Å

PDB-8vno:
Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 600s
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-8vnp:
Homing endonuclease I-PpoI-DNA complex at pH6.0 (K+ MES) with 0.2 M sodium malonate
Method: X-RAY DIFFRACTION / Resolution: 1.79 Å

PDB-8vnq:
Homing endonuclease H98A I-PpoI-DNA complex at pH6.0 (K+ MES) with 1 mM Mn2+ for 1800s
Method: X-RAY DIFFRACTION / Resolution: 1.93 Å

PDB-8vnr:
Homing endonuclease H98A I-PpoI-DNA complex at pH6.0 (K+ MES) with 1 mM Mn2+ for 600s and then 100 mM imidazole for 15 hrs
Method: X-RAY DIFFRACTION / Resolution: 1.98 Å

PDB-8vns:
Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 200 mM Mn2+ for 600s
Method: X-RAY DIFFRACTION / Resolution: 2.11 Å

PDB-8vnt:
Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mg2+ for 1800s
Method: X-RAY DIFFRACTION / Resolution: 1.62 Å

Chemicals

ChemComp-NA:
Unknown entry

ChemComp-GOL:
GLYCEROL

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-MG:
Unknown entry

ChemComp-MN:
Unknown entry

Source
  • physarum polycephalum (eukaryote)
  • synthetic construct (others)
KeywordsHYDROLASE / Intron encoded homing endonuclease I-PpoI / HYDROLASE/DNA / HYDROLASE-DNA complex

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