5akn

THE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA NICKED IN THE non-CODING STRAND B AND IN THE PRESENCE OF 2MM MN

Method: X-RAY DIFFRACTION D_max: 127.6 Å Quality: EXCELLENT

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

HOMING ENDONUCLEASE I-DMOI

DESULFUROCOCCUS MOBILIS

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 Monomer Protein × 1 DNA 4 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain A； UniProt 2–188	Mutation：YES	5'-D(GPCPCPTPTPGPCPCPGPGPGPTPAPAP)-3' × 1 5'-D(GPTPTPCPCPGPGPCPGPCPGP)-3 × 1 D(CPGPCPGPCPCPGPGPAPAPCPTPTPAPCP)-3' × 1 5'-D(CPCPGPGPCPAPAPGPGPCP)-3' × 1 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.75 Å R-free 0.236
2	Protein–DNA Monomer Protein × 1 DNA 3 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain F； UniProt 2–188	Mutation：YES	5'-D(GPCPCPTPTPGPCPCPGPGPGPTPAPAP)-3' × 1 5'-D(CPCPGPGPCPAPAPGPGPCP)-3' × 1 ;5'-D(GPTPTPCPCPGPGPCPGPCPGPCPGPCP GPCPCPGPGPAPAPCPTPTPAPCP)-3' ; × 1 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.75 Å R-free 0.236
3	Protein–DNA Monomer Protein × 1 DNA 3 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain K； UniProt 2–188	Mutation：YES	5'-D(CPCPGPGPCPAPAPGPGPCP)-3' × 1 ;5'-D(GPTPTPCPCPGPGPCPGPCPGPCPGPCP GPCPCPGPGPAPAPCPTPTPAPCP)-3' ; × 1 ;5'-D(GPCPCPTPTPGPCPCPGPGPGPTPAPAP CPGPCPGPCPCPGPGPAPAPCPTPTPAP*C)-3' ; × 1 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.75 Å R-free 0.236

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 5AKN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B24 I-DMOI, INTRON-ENCODED ENDONUCLEASE Deposited 1998-12-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–188（188 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；HANGING DROP VAPOR-DIFFUSION METHOD: 4UL I-DMOI PROTEIN 1UL 20MM N-OCTYL-B- GLUCOPYRANOSIDE 4UL PRECIPITATING BUFFER: 30% PEG 3350 200MM SODIUM ACETATE 100MM TRIS-HCL PH 8.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.20 Å R-free 0.324
2VS7 The crystal structure of I-DmoI in complex with DNA and Ca Deposited 2008-04-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 2–188（187 aa） Fragment：RESIDUES 2-188	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 5.6% PEG 4000, 0.07M SODIUM ACETATE, 30% GLYCEROL	Resolution 2.05 Å R-free 0.228
2VS7 The crystal structure of I-DmoI in complex with DNA and Ca Deposited 2008-04-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 2–188（187 aa） Fragment：RESIDUES 2-188	Not recorded	CA CALCIUM ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 5.6% PEG 4000, 0.07M SODIUM ACETATE, 30% GLYCEROL	Resolution 2.05 Å R-free 0.228
2VS7 The crystal structure of I-DmoI in complex with DNA and Ca Deposited 2008-04-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain G 2–188（187 aa） Fragment：RESIDUES 2-188	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 5.6% PEG 4000, 0.07M SODIUM ACETATE, 30% GLYCEROL	Resolution 2.05 Å R-free 0.228
2VS8 The crystal structure of I-DmoI in complex with DNA and Mn Deposited 2008-04-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain A 2–188（187 aa） Fragment：RESIDUES 2-188	Not recorded	MN MANGANESE (II) ION × 2 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions 5.6% PEG 4000, 0.07M SODIUM ACETATE, PH 4.6-5.5, 30% GLYCEROL.	Resolution 2.10 Å R-free 0.248
2VS8 The crystal structure of I-DmoI in complex with DNA and Mn Deposited 2008-04-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain F 2–188（187 aa） Fragment：RESIDUES 2-188	Not recorded	MN MANGANESE (II) ION × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 5.6% PEG 4000, 0.07M SODIUM ACETATE, PH 4.6-5.5, 30% GLYCEROL.	Resolution 2.10 Å R-free 0.248
2VS8 The crystal structure of I-DmoI in complex with DNA and Mn Deposited 2008-04-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain K 2–188（187 aa） Fragment：RESIDUES 2-188	Not recorded	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions 5.6% PEG 4000, 0.07M SODIUM ACETATE, PH 4.6-5.5, 30% GLYCEROL.	Resolution 2.10 Å R-free 0.248
4D6N THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 10 DAYS INCUBATION IN 5MM MG (STATE 7) Deposited 2014-11-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain K 2–188（187 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.35 Å R-free 0.217
4D6N THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 10 DAYS INCUBATION IN 5MM MG (STATE 7) Deposited 2014-11-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain F 2–188（187 aa）	Not recorded	MG MAGNESIUM ION × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.35 Å R-free 0.217
4D6N THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 10 DAYS INCUBATION IN 5MM MG (STATE 7) Deposited 2014-11-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain A 2–188（187 aa）	Not recorded	MG MAGNESIUM ION × 2 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.35 Å R-free 0.217
4D6O THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 1H INCUBATION IN 5MM MG (STATE 2) Deposited 2014-11-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 2–188（187 aa）	Not recorded	MG MAGNESIUM ION × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.20 Å R-free 0.220
4D6O THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 1H INCUBATION IN 5MM MG (STATE 2) Deposited 2014-11-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain G 2–188（187 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.20 Å R-free 0.220
4D6O THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 1H INCUBATION IN 5MM MG (STATE 2) Deposited 2014-11-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 2–188（187 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.20 Å R-free 0.220
4UN7 THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA BEFORE INCUBATION IN 5MM MN (STATE 1) Deposited 2014-05-26	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 2–188（187 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6	Resolution 2.70 Å R-free 0.232
4UN7 THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA BEFORE INCUBATION IN 5MM MN (STATE 1) Deposited 2014-05-26	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 2–188（187 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6	Resolution 2.70 Å R-free 0.232
4UN7 THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA BEFORE INCUBATION IN 5MM MN (STATE 1) Deposited 2014-05-26	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain G 2–188（187 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6	Resolution 2.70 Å R-free 0.232
4UN8 THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 1H INCUBATION IN 5MM MN (STATE 2) Deposited 2014-05-26	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6	Resolution 2.60 Å R-free 0.223
4UN8 THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 1H INCUBATION IN 5MM MN (STATE 2) Deposited 2014-05-26	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain G 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6	Resolution 2.60 Å R-free 0.223
4UN8 THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 1H INCUBATION IN 5MM MN (STATE 2) Deposited 2014-05-26	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6	Resolution 2.60 Å R-free 0.223
4UN9 THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 8H INCUBATION IN 5MM MN (STATE 3) Deposited 2014-05-26	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain G 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6	Resolution 2.73 Å R-free 0.220
4UN9 THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 8H INCUBATION IN 5MM MN (STATE 3) Deposited 2014-05-26	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6	Resolution 2.73 Å R-free 0.220
4UN9 THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 8H INCUBATION IN 5MM MN (STATE 3) Deposited 2014-05-26	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6	Resolution 2.73 Å R-free 0.220
4UNA THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 2 DAYS INCUBATION IN 5MM MN (STATE 4) Deposited 2014-05-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PH 6	Resolution 2.30 Å R-free 0.219
4UNA THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 2 DAYS INCUBATION IN 5MM MN (STATE 4) Deposited 2014-05-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain G 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PH 6	Resolution 2.30 Å R-free 0.219
4UNA THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 2 DAYS INCUBATION IN 5MM MN (STATE 4) Deposited 2014-05-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain D 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PH 6	Resolution 2.30 Å R-free 0.219
4UNB THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 6 DAYS INCUBATION IN 5MM MN (STATE 5) Deposited 2014-05-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain G 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PH 6	Resolution 2.55 Å R-free 0.221
4UNB THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 6 DAYS INCUBATION IN 5MM MN (STATE 5) Deposited 2014-05-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain A 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PH 6	Resolution 2.55 Å R-free 0.221
4UNB THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 6 DAYS INCUBATION IN 5MM MN (STATE 5) Deposited 2014-05-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain D 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PH 6	Resolution 2.55 Å R-free 0.221
4UNC THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 8 DAYS INCUBATION IN 5MM MN (STATE 6) Deposited 2014-05-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain D 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PH 6	Resolution 2.30 Å R-free 0.225
4UNC THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 8 DAYS INCUBATION IN 5MM MN (STATE 6) Deposited 2014-05-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain A 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PH 6	Resolution 2.30 Å R-free 0.225
4UNC THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 8 DAYS INCUBATION IN 5MM MN (STATE 6) Deposited 2014-05-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain G 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PH 6	Resolution 2.30 Å R-free 0.225
4UT0 THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 10 DAYS INCUBATION IN 5MM MN (STATE 7) Deposited 2014-07-17	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain K 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PH 6	Resolution 2.40 Å R-free 0.228
4UT0 THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 10 DAYS INCUBATION IN 5MM MN (STATE 7) Deposited 2014-07-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain F 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PH 6	Resolution 2.40 Å R-free 0.228
4UT0 THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 10 DAYS INCUBATION IN 5MM MN (STATE 7) Deposited 2014-07-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain A 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 2 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PH 6	Resolution 2.40 Å R-free 0.228
5A0W THE CRYSTAL STRUCTURE OF I-DMOI E117A IN COMPLEX WITH ITS TARGET DNA AND IN THE PRESENCE OF 2MM MN Deposited 2015-04-23	Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 2–188（187 aa）	Not recorded	CL CHLORIDE ION × 2 ACT ACETATE ION × 1 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.208
5A0W THE CRYSTAL STRUCTURE OF I-DMOI E117A IN COMPLEX WITH ITS TARGET DNA AND IN THE PRESENCE OF 2MM MN Deposited 2015-04-23	Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 2–188（187 aa）	Not recorded	CL CHLORIDE ION × 2 ACT ACETATE ION × 3 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.208
5A0W THE CRYSTAL STRUCTURE OF I-DMOI E117A IN COMPLEX WITH ITS TARGET DNA AND IN THE PRESENCE OF 2MM MN Deposited 2015-04-23	Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain G 2–188（187 aa）	Not recorded	CL CHLORIDE ION × 3 ACT ACETATE ION × 1 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.208
5AK9 THE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA IN THE PRESENCE OF 2MM MN Deposited 2015-03-02	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.222
5AK9 THE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA IN THE PRESENCE OF 2MM MN Deposited 2015-03-02	Different mutation/modification Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain J 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.222
5AK9 THE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA IN THE PRESENCE OF 2MM MN Deposited 2015-03-02	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain E 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.222
5AKF THE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA NICKED IN THE CODING STRAND A AND IN THE PRESENCE OF 2MM MN Deposited 2015-03-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain I 2–188（187 aa）	Mutation：YES	CL CHLORIDE ION × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.45 Å R-free 0.230
5AKF THE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA NICKED IN THE CODING STRAND A AND IN THE PRESENCE OF 2MM MN Deposited 2015-03-03	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain E 2–188（187 aa）	Mutation：YES	CL CHLORIDE ION × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.45 Å R-free 0.230
5AKF THE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA NICKED IN THE CODING STRAND A AND IN THE PRESENCE OF 2MM MN Deposited 2015-03-03	Different ligand/ion Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 2–188（187 aa）	Mutation：YES	CL CHLORIDE ION × 2 ACT ACETATE ION × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.45 Å R-free 0.230
5AKM THE CRYSTAL STRUCTURE OF I-DMOI G20S IN COMPLEX WITH ITS TARGET DNA IN THE PRESENCE OF 2MM MG Deposited 2015-03-04	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain F 2–188（187 aa）	Mutation：YES	ACT ACETATE ION × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.235
5AKM THE CRYSTAL STRUCTURE OF I-DMOI G20S IN COMPLEX WITH ITS TARGET DNA IN THE PRESENCE OF 2MM MG Deposited 2015-03-04	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain K 2–188（187 aa）	Mutation：YES	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.235
5AKM THE CRYSTAL STRUCTURE OF I-DMOI G20S IN COMPLEX WITH ITS TARGET DNA IN THE PRESENCE OF 2MM MG Deposited 2015-03-04	Different ligand/ion Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric	Chain A 2–188（187 aa）	Mutation：YES	ACT ACETATE ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.235
5O6G Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI Deposited 2017-06-06	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；5-6 % PEG4000, 0.07 M NaAc pH = 4.6-5.5 and 30% Glycerol	Resolution 2.75 Å R-free 0.232
5O6G Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI Deposited 2017-06-06	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；5-6 % PEG4000, 0.07 M NaAc pH = 4.6-5.5 and 30% Glycerol	Resolution 2.75 Å R-free 0.232
5O6G Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI Deposited 2017-06-06	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain G 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；5-6 % PEG4000, 0.07 M NaAc pH = 4.6-5.5 and 30% Glycerol	Resolution 2.75 Å R-free 0.232
5O6I Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI Deposited 2017-06-06	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；5-6 % PEG4000, 0.07 M NaAc pH = 4.6-5.5 and 30% Glycerol	Resolution 2.25 Å R-free 0.228
5O6I Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI Deposited 2017-06-06	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain F 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；5-6 % PEG4000, 0.07 M NaAc pH = 4.6-5.5 and 30% Glycerol	Resolution 2.25 Å R-free 0.228
5O6I Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI Deposited 2017-06-06	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain K 2–188（187 aa）	Not recorded	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；5-6 % PEG4000, 0.07 M NaAc pH = 4.6-5.5 and 30% Glycerol	Resolution 2.25 Å R-free 0.228

18 other PDB entries and 52 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DMO1_DESMO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–188； UniProt 2–188 Author chain F； PDBConstruct 2–188； UniProt 2–188 Author chain K； PDBConstruct 2–188； UniProt 2–188

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	5akn
Deposition date deposition_date	2015-03-04
Structure title title	THE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA NICKED IN THE non-CODING STRAND B AND IN THE PRESENCE OF 2MM MN
Keywords keywords	HYDROLASE-DNA COMPLEX, HYDROLASE, GENE TARGETING, GENETICS, PROTEIN-DNA INTERACTION, HOMING ENDONUCLEASES; HYDROLASE/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	38.97 Å
Radius of gyration Rg (electron density) rg_electron	38.77 Å
Forward intensity I(0) i0	291438000.00
Molecular weight molecular_weight	110360.0 kDa
Excluded volume excluded_volume	125920 Å³
Envelope volume envelope_volume	180840 Å³
Hydration-shell volume shell_volume	39233 Å³
Envelope diameter envelope_diameter	126.4 Å
Shell Rg shell_rg	44.18 Å
Envelope Rg envelope_rg	37.86 Å
Shape Rg shape_rg	38.76 Å
Total Rg total_rg	39.06 Å
Total atoms total_atoms	7567
Residues n_residues	695
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	127.6 Å
Rg (real space) rg_real	39.00 Å
Rg uncertainty (real space) rg_real_error	1.04 Å
I(0) (real space) i0_real	2.9140e+08
I(0) uncertainty (real space) i0_real_error	4.6600e+06
Rg (reciprocal space) rg_reciprocal	38.99 Å
I(0) (reciprocal space) i0_reciprocal	291400000.0000
Solution quality estimate total_estimate	0.9026
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	46.7 Å
Skewness Skewness skewness	0.223
Kurtosis Kurtosis kurtosis	-0.608
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6767000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.895

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	HOMING ENDONUCLEASE I-DMOI
Molecular weight formula_weight	23210.0 kDa
EC 编号 ec_number	3.1.-.-
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F,K
Atom count atom_count	7873

AHNNENVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITAKSENLIKQHIAPLMQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANMLERIRLFNMREQIAFIKGLYVAEGDMTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGVYVLNISLRDRIKFVHTILSSHLNPLPPEAAALEHHHHHH

来源 Source

来源生物 organism	DESULFUROCOCCUS MOBILIS
NCBI Class编号 ncbi_taxonomy_id	2274
宿主生物 host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 2 Entity 2 polymer

Description description	5'-D(GPCPCPTPTPGPCPCPGPGPGPTPAPAP)-3'
Molecular weight formula_weight	4296.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,G

GCCTTGCCGGGTAA

Entity 3 Entity 3 polymer

Description description	5'-D(GPTPTPCPCPGPGPCPGPCP*GP)-3
Molecular weight formula_weight	3366.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

GTTCCGGCGCG

Entity 4 Entity 4 polymer

Description description	D(CPGPCPGPCPCPGPGPAPAPCPTPTPAP*CP)-3'
Molecular weight formula_weight	4555.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

CGCGCCGGAACTTAC

Entity 5 Entity 5 polymer

Description description	5'-D(CPCPGPGPCPAPAPGPGPCP)-3'
Molecular weight formula_weight	3055.0 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,J,O

CCGGCAAGGC

Entity 6 Entity 6 polymer

Description description	;5'-D(GPTPTPCPCPGPGPCPGPCPGPCPGPCP GPCPCPGPGPAPAPCPTPTPAPCP)-3' ;
Molecular weight formula_weight	7966.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H,M

GTTCCGGCGCGCGCGCCGGAACTTAC

Entity 7 Entity 7 polymer

Description description	;5'-D(GPCPCPTPTPGPCPCPGPGPGPTPAPAP CPGPCPGPCPCPGPGPAPAPCPTPTPAP*C)-3' ;
Molecular weight formula_weight	8896.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	L

GCCTTGCCGGGTAACGCGCCGGAACTTAC

Entity 8 Entity 8 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	192

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5aknA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	28 — Endonuclease I-creI
Homologous superfamily homologous superfamily	10 — Homing endonucleases

Domain ID domain_id	5aknA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	28 — Endonuclease I-creI
Homologous superfamily homologous superfamily	10 — Homing endonucleases

Domain ID domain_id	5aknF01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	28 — Endonuclease I-creI
Homologous superfamily homologous superfamily	10 — Homing endonucleases

Domain ID domain_id	5aknF02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	28 — Endonuclease I-creI
Homologous superfamily homologous superfamily	10 — Homing endonucleases

Domain ID domain_id	5aknK01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	28 — Endonuclease I-creI
Homologous superfamily homologous superfamily	10 — Homing endonucleases

Domain ID domain_id	5aknK02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	28 — Endonuclease I-creI
Homologous superfamily homologous superfamily	10 — Homing endonucleases

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8. Citations (1)

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Unit-cell length a length_a	107.100 Å
Unit-cell length b length_b	70.340 Å
Unit-cell length c length_c	107.170 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	119.81 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	46.490 Å
R factor r_factor	0.1780
R_work r_work	0.1750
R_free r_free	0.2360

fit	/app/data/saxs_computation/ak/5akn/5akn.fit
pddf	/app/data/pr_computation/ak/5akn/5akn.pr.out
profile	/app/data/saxs_computation/ak/5akn/5akn.dat

THE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA NICKED IN THE non-CODING STRAND B AND IN THE PRESENCE OF 2MM MN

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

HOMING ENDONUCLEASE I-DMOI

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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

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

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)