8VMT

Homing endonuclease I-PpoI-DNA complex:reaction at pH7.0 (K+ MES) with 500 uM Mg2+ for 160s


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s

Chang, C.Gao, Y.

To be published.

Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Intron-encoded endonuclease I-PpoIC [auth A],
D [auth B]
162Physarum polycephalumMutation(s): 0 
EC: 3.1
UniProt
Find proteins for Q94702 (Physarum polycephalum)
Explore Q94702 
Go to UniProtKB:  Q94702
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94702
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*TP*CP*A)-3')A [auth C],
B [auth D]
21synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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G [auth C],
J [auth D],
M [auth A],
N [auth A],
Q [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

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K [auth A],
L [auth A],
O [auth B],
P [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

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E [auth C],
H [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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F [auth C],
I [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.58α = 90
b = 113.58β = 90
c = 87.99γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRR190046
Welch FoundationUnited StatesC-2033-20200401
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32 GM008280

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release