1evw

L116A MUTANT OF THE HOMING ENDONUCLEASE I-PPOI COMPLEXED TO HOMING SITE DNA.

Method: X-RAY DIFFRACTION D_max: 129.6 Å Quality: GOOD

▼

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

I-PPOI HOMING ENDONUCLEASE

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 4 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain A； UniProt 1–163 Chain B； UniProt 1–163	Mutation：L116A	;DNA (5'-D(TPGPGPCPTPAPCPCPTPTPAPA)-3') ; × 1 ;DNA (5'-D(PGPAPGPAPGPTPCPA)-3') ; × 1 ;DNA (5'-D(TPGPAPCPTPCPTPCPTPTPAPA)-3') ; × 1 ;DNA (5'-D(PGPGPTPAPGPCPCPA)-3') ; × 1 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
2	Protein–DNA Homooligomer Protein × 2 DNA 4 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain C； UniProt 1–163 Chain D； UniProt 1–163	Mutation：L116A	;DNA (5'-D(TPGPGPCPTPAPCPCPTPTPAPA)-3') ; × 1 ;DNA (5'-D(PGPAPGPAPGPTPCPA)-3') ; × 1 ;DNA (5'-D(TPGPAPCPTPCPTPCPTPTPAPA)-3') ; × 1 ;DNA (5'-D(PGPGPTPAPGPCPCPA)-3') ; × 1 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

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 1EVW	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 mutation/modification 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 mutation/modification Different oligomeric state 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 oligomeric state 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 mutation/modification Different oligomeric state 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
1EVX APO CRYSTAL STRUCTURE OF THE HOMING ENDONUCLEASE, I-PPOI 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 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
1IPP HOMING ENDONUCLEASE/DNA COMPLEX Deposited 1998-03-19	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: tetrameric	Chain A 23–185（163 aa） Chain B 23–185（163 aa）	Not recorded	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
2O6M H98Q mutant of the homing endonuclease I-PPOI complexed with DNA Deposited 2006-12-07	Different mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification 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 mutation/modification Different oligomeric state 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 49 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PPO1_PHYPO
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain A； PDBConstruct 1–163； UniProt 1–163 Author chain B； PDBConstruct 1–163； UniProt 1–163 Author chain C； PDBConstruct 1–163； UniProt 1–163 Author chain D； PDBConstruct 1–163； UniProt 1–163

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1evw
Deposition date deposition_date	2000-04-20
Structure title title	L116A MUTANT OF THE HOMING ENDONUCLEASE I-PPOI COMPLEXED TO HOMING SITE DNA.
Keywords keywords	DNA binding B-sheets; C-terminal exchanged dimer interface; bent DNA, Hydrolase-DNA COMPLEX; Hydrolase/DNA
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	37.27 Å
Radius of gyration Rg (electron density) rg_electron	37.84 Å
Forward intensity I(0) i0	202593000.00
Molecular weight molecular_weight	95699.0 kDa
Excluded volume excluded_volume	111330 Å³
Envelope volume envelope_volume	161070 Å³
Hydration-shell volume shell_volume	37901 Å³
Envelope diameter envelope_diameter	132.5 Å
Shell Rg shell_rg	40.80 Å
Envelope Rg envelope_rg	36.95 Å
Shape Rg shape_rg	37.86 Å
Total Rg total_rg	37.96 Å
Total atoms total_atoms	6612
Residues n_residues	728
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

▼

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

Maximum dimension Dmax dmax	129.6 Å
Rg (real space) rg_real	37.54 Å
Rg uncertainty (real space) rg_real_error	1.52 Å
I(0) (real space) i0_real	2.0260e+08
I(0) uncertainty (real space) i0_real_error	4.1490e+06
Rg (reciprocal space) rg_reciprocal	37.38 Å
I(0) (reciprocal space) i0_reciprocal	202600000.0000
Solution quality estimate total_estimate	0.8544
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	46.3 Å
Skewness Skewness skewness	0.439
Kurtosis Kurtosis kurtosis	-0.364
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12260000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.805; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.857; Smooth: 0.830

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(TPGPGPCPTPAPCPCPTPTPAPA)-3') ;
Molecular weight formula_weight	3637.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,G
Atom count atom_count	6612

TGGCTACCTTAA

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PGPAPGPAPGPTPCPA)-3') ;
Molecular weight formula_weight	2475.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	M,N

GAGAGTCA

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(TPGPAPCPTPCPTPCPTPTPAPA)-3') ;
Molecular weight formula_weight	3612.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F,H

TGACTCTCTTAA

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D(PGPGPTPAPGPCPCPA)-3') ;
Molecular weight formula_weight	2451.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	O,P

GGTAGCCA

Entity 5 Entity 5 polymer

Description description	I-PPOI HOMING ENDONUCLEASE
Molecular weight formula_weight	17769.2 kDa
Mutation mutation	L116A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

MALTNAQILAVIDSWEETVGQFPVITHHVPLGGGLQGTLHCYEIPLAAPYGVGFAKNGPTRWQYKRTINQVVHRWGSHTVPFLLEPDNINGKTCTASHLCHNTRCHNPLHLCWESADDNKGRNWCPGPNGGCVHAVVCLRQGPLYGPGATVAGPQQRGSHFVV

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

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

▼

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1evwa_
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	d1evwb_
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	d1evwc_
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	d1evwd_
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 (4 domains)

Domain ID domain_id	1evwA00
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	1evwB00
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	1evwC00
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	1evwD00
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	182.000 Å
Unit-cell length b length_b	73.100 Å
Unit-cell length c length_c	92.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2730
R_free r_free	0.3200

fit	/app/data/saxs_computation/ev/1evw/1evw.fit
pddf	/app/data/pr_computation/ev/1evw/1evw.pr.out
profile	/app/data/saxs_computation/ev/1evw/1evw.dat

L116A MUTANT OF THE HOMING ENDONUCLEASE I-PPOI COMPLEXED TO HOMING SITE DNA.

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

I-PPOI HOMING ENDONUCLEASE

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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)