8vmv

Homing endonuclease I-PpoI-DNA complex:reaction at pH7.0 (K+ MES) with 500 uM Mg2+ for 600s

Method: X-RAY DIFFRACTION D_max: 78.2 Å Quality: EXCELLENT

▼

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 4 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain A； UniProt 2–163 Chain B； UniProt 2–163	Not recorded	;DNA (5'-D(TPTPGPAPCPTPCPTPCPTPTPAPA)-3') ; × 2 ;DNA (5'-D(PGPAPGPAPGPTPCPA)-3') ; × 2 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

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 8VMV	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 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 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 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）	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 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
1EVW L116A MUTANT OF THE HOMING ENDONUCLEASE I-PPOI COMPLEXED TO HOMING SITE DNA. Deposited 2000-04-20	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 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 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 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 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 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 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 oligomeric state Different ligand/ion 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 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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
8VMW Homing endonuclease I-PpoI-DNA complex:ground state at pH6.0 (K+ MES) with Na+ Deposited 2024-01-13	Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–162； UniProt 2–163 Author chain B； PDBConstruct 1–162； UniProt 2–163

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	8vmv
Deposition date deposition_date	2024-01-13
Structure title title	Homing endonuclease I-PpoI-DNA complex:reaction at pH7.0 (K+ MES) with 500 uM Mg2+ for 600s
Keywords keywords	Intron encoded homing endonuclease I-PpoI, HYDROLASE, 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	24.82 Å
Radius of gyration Rg (electron density) rg_electron	24.53 Å
Forward intensity I(0) i0	55208000.00
Molecular weight molecular_weight	48662.0 kDa
Excluded volume excluded_volume	56771 Å³
Envelope volume envelope_volume	70937 Å³
Hydration-shell volume shell_volume	24698 Å³
Envelope diameter envelope_diameter	80.6 Å
Shell Rg shell_rg	31.30 Å
Envelope Rg envelope_rg	24.57 Å
Shape Rg shape_rg	24.54 Å
Total Rg total_rg	25.13 Å
Total atoms total_atoms	3359
Residues n_residues	364
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	78.2 Å
Rg (real space) rg_real	24.85 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	5.5210e+07
I(0) uncertainty (real space) i0_real_error	7.7860e+05
Rg (reciprocal space) rg_reciprocal	24.85 Å
I(0) (reciprocal space) i0_reciprocal	55210000.0000
Solution quality estimate total_estimate	0.9035
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.3 Å
Skewness Skewness skewness	0.344
Kurtosis Kurtosis kurtosis	-0.494
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5502000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.967

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(TPTPGPAPCPTPCPTPCPTPTPAP*A)-3') ;
Molecular weight formula_weight	3916.6 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	3779

TTGACTCTCTTAA

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	c,d

GAGAGTCA

Entity 3 Entity 3 polymer

Description description	Intron-encoded endonuclease I-PpoI
Molecular weight formula_weight	17680.0 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

ALTNAQILAVIDSWEETVGQFPVITHHVPLGGGLQGTLHCYEIPLAAPYGVGFAKNGPTRWQYKRTINQVVHRWGSHTVPFLLEPDNINGKTCTASHLCHNTRCHNPLHLCWESLDDNKGRNWCPGPNGGCVHAVVCLRQGPLYGPGATVAGPQQRGSHFVV

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 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

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	4

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	353

▶

8. Citations (2)

▶

Unit-cell length a length_a	113.580 Å
Unit-cell length b length_b	113.580 Å
Unit-cell length c length_c	87.990 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	1.590 Å
Low-resolution limit resolution_low	42.930 Å
R factor r_factor	0.1799
R_work r_work	0.1790
R_free r_free	0.1964

fit	/app/data/saxs_computation/vm/8vmv/8vmv.fit
pddf	/app/data/pr_computation/vm/8vmv/8vmv.pr.out
profile	/app/data/saxs_computation/vm/8vmv/8vmv.dat

Homing endonuclease I-PpoI-DNA complex:reaction at pH7.0 (K+ MES) with 500 uM Mg2+ for 600s

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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)