1ipp

HOMING ENDONUCLEASE/DNA COMPLEX

Method: X-RAY DIFFRACTION D_max: 77.8 Å Quality: EXCELLENT

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1. Protein Identity and Related Structures Protein Identity & Related Structures

INTRON-ENCODED ENDONUCLEASE I-PPOI

Physarum polycephalum

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 23–185 Chain B； UniProt 23–185	Not recorded	;DNA (5'-D(TPTPGPAPCPTPCPTPCPTPTPAPAPGPAPGPAPGPTPCP*A)-3') ; × 2 CD CADMIUM ION × 4 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5.4；THE CRYSTALS WERE GROWN FROM A 2:1 MOLAR RATIO SOLUTION OF PROTEIN AND DNA SUPPLEMENTED WITH 2.5 MM EDTA AND 5 MM SPERMINE. THE COMPLEX WAS CRYSTALLIZED FROM 21 - 27% PEG 4000, 0.1 M CITRATE, PH 5.4 - 5.8; 20 MM NACL, 2 MM EDTA., VAPOR DIFFUSION	Resolution 2.20 Å R-free 0.316

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1IPP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A73 INTRON-ENCODED ENDONUCLEASE I-PPOI COMPLEXED WITH DNA Deposited 1998-03-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 1–163（163 aa） Fragment：ENDONUCLEASE (I-PPO) ENCODED ENDONUCLEASE Chain B 1–163（163 aa） Fragment：ENDONUCLEASE (I-PPO) ENCODED ENDONUCLEASE	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；THE CRYSTALS WERE GROWN FROM A 2:1 MOLAR RATIO SOLUTION OF PROTEIN AND DNA SUPPLEMENTED WITH 2.5 MM EDTA AND 5 MM SPERMINE. THE COMPLEX WAS CRYSTALLIZED FROM 21 - 27% PEG 4000, 0.1 M CITRATE, PH 5.4 - 5.8, 20 MM NACL, 2 MM EDTA., pH 5.6, VAPOR DIFFUSION, HANGING DROP	Resolution 1.80 Å R-free 0.297
1A74 I-PPOL HOMING ENDONUCLEASE/DNA COMPLEX Deposited 1998-03-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–163（163 aa） Chain B 1–163（163 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；THE CRYSTALS WERE GROWN FROM A 2:1 MOLAR RATIO SOLUTION OF PROTEIN AND DNA SUPPLEMENTED WITH 2.5 MM EDTA AND 5 MM SPERMINE. THE COMPLEX WAS CRYSTALLIZED FROM 21 - 27% PEG 4000, 0.1 M CITRATE, PH 5.4 - 5.8; 20 MM NACL, 2 MM EDTA., pH 5.60, VAPOR DIFFUSION	Resolution 2.20 Å R-free 0.265
1CYQ INTRON ENCODED HOMING ENDONUCLEASE I-PPOI (H98A)/DNA HOMING SITE COMPLEX Deposited 1999-08-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Mutation：H98A Mutation：H98A	MG MAGNESIUM ION × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG 3350, SODIUM CITRATE, SODIUM CHLORIDE, SPERMINE, EDTA, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.93 Å R-free 0.235
1CZ0 INTRON ENCODED HOMING ENDONUCLEASE I-PPOI/DNA COMPLEX LACKING CATALYTIC METAL ION Deposited 1999-08-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	NA SODIUM ION × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；PEG 3350, SODIUM CITRATE, SODIUM CHLORIDE, SPERMINE, EDTA, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.10 Å R-free 0.216
1EVW L116A MUTANT OF THE HOMING ENDONUCLEASE I-PPOI COMPLEXED TO HOMING SITE DNA. Deposited 2000-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 1–163（163 aa） Chain B 1–163（163 aa）	Mutation：L116A Mutation：L116A	MG MAGNESIUM ION × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；MPD, MES pH 6.5, NaCl, MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.10 Å R-free 0.320
1EVW L116A MUTANT OF THE HOMING ENDONUCLEASE I-PPOI COMPLEXED TO HOMING SITE DNA. Deposited 2000-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain C 1–163（163 aa） Chain D 1–163（163 aa）	Mutation：L116A Mutation：L116A	MG MAGNESIUM ION × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；MPD, MES pH 6.5, NaCl, MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.10 Å R-free 0.320
1EVX APO CRYSTAL STRUCTURE OF THE HOMING ENDONUCLEASE, I-PPOI Deposited 2000-04-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	ZN ZINC ION × 4 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；ammonium sulfate, PEG 8K, sodium cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 2.00 Å R-free 0.229
2O6M H98Q mutant of the homing endonuclease I-PPOI complexed with DNA Deposited 2006-12-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–163（163 aa） Chain B 1–163（163 aa）	Mutation：H98Q Mutation：H98Q	MG MAGNESIUM ION × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；0.1 M Citrate, pH 5.2-5.8, 20 mM NaCl, 2 mM EDTA, 20-30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 2.30 Å R-free 0.244
8VMO Homing endonuclease I-PpoI-DNA complex:ground state at pH7.0 (K+ MES) with Na+ Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.68 Å R-free 0.189
8VMP Homing endonuclease I-PpoI-DNA complex:reaction at pH7.0 (K+ MES) with 500 uM Mg2+ for 10s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.45 Å R-free 0.185
8VMQ Homing endonuclease I-PpoI-DNA complex:reaction at pH7.0 (K+ MES) with 500 uM Mg2+ for 20s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	MG MAGNESIUM ION × 1 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.48 Å R-free 0.188
8VMR Homing endonuclease I-PpoI-DNA complex:reaction at pH7.0 (K+ MES) with 500 uM Mg2+ for 40s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	MG MAGNESIUM ION × 1 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.50 Å R-free 0.194
8VMS Homing endonuclease I-PpoI-DNA complex:reaction at pH7.0 (K+ MES) with 500 uM Mg2+ for 80s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	MG MAGNESIUM ION × 2 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.42 Å R-free 0.189
8VMT Homing endonuclease I-PpoI-DNA complex:reaction at pH7.0 (K+ MES) with 500 uM Mg2+ for 160s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	MG MAGNESIUM ION × 2 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.48 Å R-free 0.196
8VMU Homing endonuclease I-PpoI-DNA complex:reaction at pH7.0 (K+ MES) with 500 uM Mg2+ for 320s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	MG MAGNESIUM ION × 2 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.52 Å R-free 0.194
8VMV Homing endonuclease I-PpoI-DNA complex:reaction at pH7.0 (K+ MES) with 500 uM Mg2+ for 600s Deposited 2024-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	GOL GLYCEROL × 5 MG MAGNESIUM ION × 2 NA SODIUM ION × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.59 Å R-free 0.196
8VMW Homing endonuclease I-PpoI-DNA complex:ground state at pH6.0 (K+ MES) with Na+ Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.60 Å R-free 0.198
8VMX Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mg2+ for 10s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.45 Å R-free 0.184
8VMY Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mg2+ for 20s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	NA SODIUM ION × 2 MG MAGNESIUM ION × 1 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.53 Å R-free 0.189
8VMZ Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mg2+ for 40s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	MG MAGNESIUM ION × 2 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.57 Å R-free 0.196
8VN0 Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mg2+ for 80s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	MG MAGNESIUM ION × 2 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.60 Å R-free 0.196
8VN1 Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mg2+ for 160s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	MG MAGNESIUM ION × 2 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.79 Å R-free 0.200
8VN2 Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mg2+ for 320s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	MG MAGNESIUM ION × 2 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.63 Å R-free 0.192
8VN3 Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mg2+ for 600s Deposited 2024-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	GOL GLYCEROL × 5 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.63 Å R-free 0.193
8VN4 Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mg2+ for 1200s Deposited 2024-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	GOL GLYCEROL × 5 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.75 Å R-free 0.202
8VN5 Homing endonuclease I-PpoI-DNA complex:ground state at pH8.0 (Tris) with Na+ Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.65 Å R-free 0.188
8VN6 Homing endonuclease I-PpoI-DNA complex:reaction at pH8.0 (Tris) with 500 uM Mg2+ for 10s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	MG MAGNESIUM ION × 2 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.54 Å R-free 0.197
8VN7 Homing endonuclease I-PpoI-DNA complex:reaction at pH8.0 (Tris) with 500 uM Mg2+ for 20s Deposited 2024-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	GOL GLYCEROL × 5 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.67 Å R-free 0.196
8VN8 Homing endonuclease I-PpoI-DNA complex:reaction at pH8.0 (Tris) with 500 uM Mg2+ for 40s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	MG MAGNESIUM ION × 2 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.60 Å R-free 0.194
8VN9 Homing endonuclease I-PpoI-DNA complex:reaction at pH8.0 (Tris) with 500 uM Mg2+ for 80s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	MG MAGNESIUM ION × 2 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.69 Å R-free 0.192
8VNA Homing endonuclease I-PpoI-DNA complex:reaction at pH8.0 (Tris) with 500 uM Mg2+ for 160s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	MG MAGNESIUM ION × 2 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.54 Å R-free 0.197
8VNB Homing endonuclease I-PpoI-DNA complex:reaction at pH8.0 (Tris) with 500 uM Mg2+ for 240s Deposited 2024-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	GOL GLYCEROL × 5 ZN ZINC ION × 4 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.72 Å R-free 0.197
8VNC Homing endonuclease I-PpoI-DNA complex:reaction at pH8.0 (Tris) with 500 uM Mg2+ for 320s Deposited 2024-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	GOL GLYCEROL × 5 ZN ZINC ION × 4 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.62 Å R-free 0.188
8VND Homing endonuclease I-PpoI-DNA complex:reaction at pH8.0 (Tris) with 500 uM Mg2+ for 600s Deposited 2024-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	GOL GLYCEROL × 5 ZN ZINC ION × 4 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.60 Å R-free 0.192
8VNE Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 10s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.57 Å R-free 0.196
8VNF Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 20s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.50 Å R-free 0.196
8VNG Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 40s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.60 Å R-free 0.192
8VNH Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 80s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.76 Å R-free 0.206
8VNJ Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 120s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.61 Å R-free 0.196
8VNK Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 160s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.61 Å R-free 0.194
8VNL Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 240s Deposited 2024-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	GOL GLYCEROL × 5 MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.64 Å R-free 0.188
8VNM Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 320s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.59 Å R-free 0.190
8VNN Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 480s Deposited 2024-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	GOL GLYCEROL × 5 MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.79 Å R-free 0.195
8VNO Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 600s Deposited 2024-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	GOL GLYCEROL × 5 MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.70 Å R-free 0.193
8VNP Homing endonuclease I-PpoI-DNA complex at pH6.0 (K+ MES) with 0.2 M sodium malonate Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.79 Å R-free 0.190
8VNQ Homing endonuclease H98A I-PpoI-DNA complex at pH6.0 (K+ MES) with 1 mM Mn2+ for 1800s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.93 Å R-free 0.210
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 Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.98 Å R-free 0.216
8VNS Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 200 mM Mn2+ for 600s Deposited 2024-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 2.11 Å R-free 0.252
8VNT Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mg2+ for 1800s Deposited 2024-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	GOL GLYCEROL × 5 ZN ZINC ION × 4 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 1.62 Å R-free 0.198
8VNU Homing endonuclease H98A I-PpoI-DNA complex at pH6.0 (K+ MES) with 70 mM Tl+ for 1800s Deposited 2024-01-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–163（162 aa） Chain B 2–163（162 aa）	Not recorded	TL THALLIUM (I) ION × 2 NA SODIUM ION × 2 GOL GLYCEROL × 5 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2 M Sodium Malonate, PEG 3350, 0.1 M MES	Resolution 2.20 Å R-free 0.219

49 other PDB entries and 50 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PPO1_PHYPO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–163； UniProt 23–185 Author chain B； PDBConstruct 1–163； UniProt 23–185

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ipp
Deposition date deposition_date	1998-03-19
Structure title title	HOMING ENDONUCLEASE/DNA COMPLEX
Keywords keywords	HOMING ENDONUCLEASE, INTRON, ZINC, DNA BINDING, PROTEIN FOLDING, TRANSCRIPTION/DNA, TRANSCRIPTION-DNA complex; TRANSCRIPTION/DNA
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.72 Å
Radius of gyration Rg (electron density) rg_electron	24.52 Å
Forward intensity I(0) i0	56210900.00
Molecular weight molecular_weight	48697.0 kDa
Excluded volume excluded_volume	56478 Å³
Envelope volume envelope_volume	70380 Å³
Hydration-shell volume shell_volume	24492 Å³
Envelope diameter envelope_diameter	81.1 Å
Shell Rg shell_rg	31.23 Å
Envelope Rg envelope_rg	24.60 Å
Shape Rg shape_rg	24.54 Å
Total Rg total_rg	25.09 Å
Total atoms total_atoms	3350
Residues n_residues	366
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	77.8 Å
Rg (real space) rg_real	24.76 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	5.6210e+07
I(0) uncertainty (real space) i0_real_error	7.6120e+05
Rg (reciprocal space) rg_reciprocal	24.75 Å
I(0) (reciprocal space) i0_reciprocal	56210000.0000
Solution quality estimate total_estimate	0.9006
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	76.6 Å
Skewness Skewness skewness	0.350
Kurtosis Kurtosis kurtosis	-0.486
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5432000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.930

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(TPTPGPAPCPTPCPTPCPTPTPAPAPGPAPGPAPGPTPCP*A)-3') ;
Molecular weight formula_weight	6437.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,D
Atom count atom_count	3897

TTGACTCTCTTAAGAGAGTCA

Entity 2 Entity 2 polymer

Description description	INTRON-ENCODED ENDONUCLEASE I-PPOI
Molecular weight formula_weight	17811.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

MALTNAQILAVIDSWEETVGQFPVITHHVPLGGGLQGTLHCYEIPLAAPYGVGFAKNGPTRWQYKRTINQVVHRWGSHTVPFLLEPDNINGKTCTASHLCHNTRCHNPLHLCWESLDDNKGRNWCPGPNGGCVHAVVCLRQGPLYGPGATVAGPQQRGSHFVV

来源 Source

来源生物 organism	Physarum polycephalum
NCBI Class编号 ncbi_taxonomy_id	5791
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	547

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ippa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.4 — His-Me finger endonucleases
Superfamily Superfamily superfamily	d.4.1 — His-Me finger endonucleases
Family Family family	d.4.1.3 — Intron-encoded homing endonucleases

Domain ID domain_id	d1ippb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.4 — His-Me finger endonucleases
Superfamily Superfamily superfamily	d.4.1 — His-Me finger endonucleases
Family Family family	d.4.1.3 — Intron-encoded homing endonucleases

CATH v4.4 (2 domains)

Domain ID domain_id	1ippA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	75 — Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Homing Intron 3 (I-ppo) Encoded Endonuclease; Chain A

Domain ID domain_id	1ippB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	75 — Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Homing Intron 3 (I-ppo) Encoded Endonuclease; Chain A

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8. Citations (2)

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Unit-cell length a length_a	113.900 Å
Unit-cell length b length_b	113.900 Å
Unit-cell length c length_c	88.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2120
R_free r_free	0.3160

fit	/app/data/saxs_computation/ip/1ipp/1ipp.fit
pddf	/app/data/pr_computation/ip/1ipp/1ipp.pr.out
profile	/app/data/saxs_computation/ip/1ipp/1ipp.dat

HOMING ENDONUCLEASE/DNA COMPLEX

1. Protein Identity and Related Structures Protein Identity & Related Structures

INTRON-ENCODED ENDONUCLEASE I-PPOI

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)