8iq0

Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized state

Method: X-RAY DIFFRACTION D_max: 128.4 Å Quality: GOOD

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

Superoxide dismutase [Cu-Zn]

OrganismNot specified

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–152 Chain B； UniProt 2–152	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25%PEG4000, 150mM ammonium sulfate and 100 mM MES	Resolution 1.88 Å R-free 0.244
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 2–152 Chain D； UniProt 2–152	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25%PEG4000, 150mM ammonium sulfate and 100 mM MES	Resolution 1.88 Å R-free 0.244
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 2–152 Chain F； UniProt 2–152	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25%PEG4000, 150mM ammonium sulfate and 100 mM MES	Resolution 1.88 Å R-free 0.244
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 2–152 Chain H； UniProt 2–152	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25%PEG4000, 150mM ammonium sulfate and 100 mM MES	Resolution 1.88 Å R-free 0.244
5	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain I； UniProt 2–152 Chain J； UniProt 2–152	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25%PEG4000, 150mM ammonium sulfate and 100 mM MES	Resolution 1.88 Å R-free 0.244
6	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain K； UniProt 2–152 Chain L； UniProt 2–152	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 SO4 SULFATE ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25%PEG4000, 150mM ammonium sulfate and 100 mM MES	Resolution 1.88 Å R-free 0.244
7	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain M； UniProt 2–152 Chain N； UniProt 2–152	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25%PEG4000, 150mM ammonium sulfate and 100 mM MES	Resolution 1.88 Å R-free 0.244
8	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain O； UniProt 2–152 Chain P； UniProt 2–152	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25%PEG4000, 150mM ammonium sulfate and 100 mM MES	Resolution 1.88 Å R-free 0.244

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 8IQ0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CB4 CRYSTAL STRUCTURE OF COPPER, ZINC SUPEROXIDE DISMUTASE Deposited 1999-02-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–152（151 aa） Chain B 2–152（151 aa）	Not recorded	CU COPPER (II) ION × 3 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；277 K；pH 6.00, temperature 277.00K	Resolution 2.30 Å R-free 0.228
1CBJ CRYSTAL STRUCTURE OF BOVINE SUPEROXIDE DISMUTASE CRYSTAL. Deposited 1999-02-26	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–152（151 aa） Chain B 2–152（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 1.65 Å R-free 0.228
1COB CRYSTAL STRUCTURE SOLUTION AND REFINEMENT OF THE SEMISYNTHETIC COBALT SUBSTITUTED BOVINE ERYTHROCYTE ENZYME SUPEROXIDE DISMUTASE AT 2.0 ANGSTROMS RESOLUTION Deposited 1992-02-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	CU COPPER (II) ION × 2 CO COBALT (II) ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1E9O Crystal structure of bovine SOD - 1 of 3 Deposited 2000-10-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	CU COPPER (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；PEG-4000, NACL, pH 4.00	Resolution 1.85 Å R-free 0.230
1E9P Crystal structure of bovine Cu, Zn SOD to 1.7 Angstrom (3 of 3) Deposited 2000-10-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	CU COPPER (II) ION × 3 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 1.70 Å R-free 0.202
1E9Q Crystal structure of bovine Cu Zn SOD - (1 of 3) Deposited 2000-10-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	CU COPPER (II) ION × 3 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 1.75 Å R-free 0.205
1Q0E Atomic resolution (1.15 ) crystal structure of bovine copper, zinc superoxide dismutase Deposited 2003-07-16	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 1–151（151 aa） Fragment：Copper, Zinc Superoxide Dismutase	Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；15 % PEG-4000, 50 mM glycyl-glycine , 100 mM NaCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.15 Å R-free 0.166
1Q0E Atomic resolution (1.15 ) crystal structure of bovine copper, zinc superoxide dismutase Deposited 2003-07-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–151（151 aa） Fragment：Copper, Zinc Superoxide Dismutase	Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；15 % PEG-4000, 50 mM glycyl-glycine , 100 mM NaCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.15 Å R-free 0.166
1SDA CRYSTAL STRUCTURE OF PEROXYNITRITE-MODIFIED BOVINE CU,ZN SUPEROXIDE DISMUTASE Deposited 1993-01-13	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain O 1–151（151 aa） Chain Y 1–151（151 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1SDA CRYSTAL STRUCTURE OF PEROXYNITRITE-MODIFIED BOVINE CU,ZN SUPEROXIDE DISMUTASE Deposited 1993-01-13	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–151（151 aa） Chain G 1–151（151 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1SXA CRYSTAL STRUCTURE OF REDUCED BOVINE ERYTHROCYTE SUPEROXIDE DISMUTASE AT 1.9 ANGSTROMS RESOLUTION Deposited 1995-03-17	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1SXB CRYSTAL STRUCTURE OF REDUCED BOVINE ERYTHROCYTE SUPEROXIDE DISMUTASE AT 1.9 ANGSTROMS RESOLUTION Deposited 1995-03-17	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1SXC CRYSTAL STRUCTURE OF REDUCED BOVINE ERYTHROCYTE SUPEROXIDE DISMUTASE AT 1.9 ANGSTROMS RESOLUTION Deposited 1995-03-17	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1SXN REDUCED BOVINE SUPEROXIDE DISMUTASE AT PH 5.0 Deposited 1997-09-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions excess nitrogen atmosphere；pH 5；20 % PEG6K, 20MM HEPES PH 5.0, SODIUM DITHIONITE (EXCESS), NITROGEN ATMOSPHERE, excess nitrogen atmosphere	Resolution 1.90 Å
1SXS Reduced bovine superoxide dismutase at pH 5.0 complexed with thiocyanate Deposited 1998-09-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	SCN THIOCYANATE ION × 2 CU COPPER (II) ION × 2 ZN ZINC ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions excess nitrogen atmosphere；pH 5；20 % PEG6K, 20MM HEPES, 100MM NASCN, PH 5.0, SODIUM DITHIONITE (EXCESS), NITROGEN ATMOSPHERE, excess nitrogen atmosphere	Resolution 2.00 Å
1SXZ Reduced bovine superoxide dismutase at pH 5.0 complexed with azide Deposited 1998-09-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 CA CALCIUM ION × 2 AZI AZIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions excess nitrogen atmosphere；pH 5；20 % PEG6K, 20MM HEPES PH 5.0, SODIUM DITHIONITE (EXCESS), NITROGEN ATMOSPHERE, excess nitrogen atmosphere	Resolution 2.05 Å
2AEO Crystal structure of cisplatinated bovine Cu,Zn superoxide dismutase Deposited 2005-07-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	CU COPPER (II) ION × 4 ZN ZINC ION × 4 CPT Cisplatin × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；50mM Tris HCl, 18% PEG 4000, 20% 2-propanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.236
2SOD DETERMINATION AND ANALYSIS OF THE 2 ANGSTROM STRUCTURE OF COPPER, ZINC SUPEROXIDE DISMUTASE Deposited 1980-03-25	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain O 1–151（151 aa） Chain Y 1–151（151 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
2SOD DETERMINATION AND ANALYSIS OF THE 2 ANGSTROM STRUCTURE OF COPPER, ZINC SUPEROXIDE DISMUTASE Deposited 1980-03-25	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–151（151 aa） Chain G 1–151（151 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
2Z7U Crystal Structure of H2O2 treated Cu,Zn-SOD Deposited 2007-08-28	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–152（151 aa） Chain B 2–152（151 aa）	Not recorded	ZN ZINC ION × 2 CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；295 K；20% (w/v) PEG 4000, 20% (w/v) iso-propanol, 0.09M MES, 1mM EDTA, pH 6.4-6.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.10 Å R-free 0.238
2Z7W Crystal Structure of H2O2 treated Cu,Zn-SOD Deposited 2007-08-29	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–152（151 aa） Chain B 2–152（151 aa）	Not recorded	ZN ZINC ION × 2 CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；295 K；20% (w/v) PEG 4000, 20% (w/v) iso-propanol, 0.09M MES, 1mM EDTA, pH 6.4-6.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.80 Å R-free 0.234
2Z7Y Crystal Structure of H2O2 treated Cu,Zn-SOD Deposited 2007-08-30	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–152（151 aa） Chain B 2–152（151 aa）	Not recorded	ZN ZINC ION × 2 CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；295 K；20% (w/v) PEG 4000, 20% (w/v) iso-propanol, 0.09M MES, 1mM EDTA, pH 6.4-6.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.55 Å R-free 0.210
2Z7Z Crystal Structure of H2O2 treated Cu,Zn-SOD Deposited 2007-08-30	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–152（151 aa） Chain B 2–152（151 aa）	Not recorded	ZN ZINC ION × 2 CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；295 K；20% (w/v) PEG 4000, 20% (w/v) iso-propanol, 0.09M MES, 1mM EDTA, pH 6.4-6.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.85 Å R-free 0.228
2ZOW Crystal Structure of H2O2 treated Cu,Zn-SOD Deposited 2008-06-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–152（151 aa） Chain B 2–152（151 aa）	Not recorded	ZN ZINC ION × 2 CU1 COPPER (I) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；295 K；20% (w/v) PEG 4000, 20% (w/v) iso-propanol, 0.09M MES, 1mM EDTA, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.45 Å R-free 0.221
3HW7 High pressure (0.57 GPa) crystal structure of bovine copper, zinc superoxide dismutase at 2.0 angstroms Deposited 2009-06-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–152（151 aa） Chain B 2–152（151 aa）	Not recorded	CU1 COPPER (I) ION × 2 ZN ZINC ION × 2 CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.218
3SOD CHANGES IN CRYSTALLOGRAPHIC STRUCTURE AND THERMOSTABILITY OF A CU,ZN SUPEROXIDE DISMUTASE MUTANT RESULTING FROM THE REMOVAL OF BURIED CYSTEINE Deposited 1990-06-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain O 1–151（151 aa） Chain Y 1–151（151 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
3SOD CHANGES IN CRYSTALLOGRAPHIC STRUCTURE AND THERMOSTABILITY OF A CU,ZN SUPEROXIDE DISMUTASE MUTANT RESULTING FROM THE REMOVAL OF BURIED CYSTEINE Deposited 1990-06-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–151（151 aa） Chain G 1–151（151 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
8IQ1 Crystal structure of hydrogen sulfide-bound superoxide dismutase in reduced state Deposited 2023-03-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–152（151 aa） Chain B 2–152（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 5 H2S HYDROSULFURIC ACID × 1 SO4 SULFATE ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；25% PEG 4000, 150 mM amimonium sulfate and 100 mM MES, pH 5.5	Resolution 1.80 Å R-free 0.217
8IQ1 Crystal structure of hydrogen sulfide-bound superoxide dismutase in reduced state Deposited 2023-03-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 2–152（151 aa） Chain D 2–152（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 4 SO4 SULFATE ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；25% PEG 4000, 150 mM amimonium sulfate and 100 mM MES, pH 5.5	Resolution 1.80 Å R-free 0.217
8IQ1 Crystal structure of hydrogen sulfide-bound superoxide dismutase in reduced state Deposited 2023-03-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 2–152（151 aa） Chain F 2–152（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 4 H2S HYDROSULFURIC ACID × 1 CL CHLORIDE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；25% PEG 4000, 150 mM amimonium sulfate and 100 mM MES, pH 5.5	Resolution 1.80 Å R-free 0.217
8IQ1 Crystal structure of hydrogen sulfide-bound superoxide dismutase in reduced state Deposited 2023-03-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 2–152（151 aa） Chain H 2–152（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 5 H2S HYDROSULFURIC ACID × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；25% PEG 4000, 150 mM amimonium sulfate and 100 mM MES, pH 5.5	Resolution 1.80 Å R-free 0.217

24 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SODC_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–151； UniProt 2–152 Author chain B； PDBConstruct 1–151； UniProt 2–152 Author chain C； PDBConstruct 1–151； UniProt 2–152 Author chain D； PDBConstruct 1–151； UniProt 2–152 Author chain E； PDBConstruct 1–151； UniProt 2–152 Author chain F； PDBConstruct 1–151； UniProt 2–152 Author chain G； PDBConstruct 1–151； UniProt 2–152 Author chain H； PDBConstruct 1–151； UniProt 2–152 Author chain I； PDBConstruct 1–151； UniProt 2–152 Author chain J； PDBConstruct 1–151； UniProt 2–152 Author chain K； PDBConstruct 1–151； UniProt 2–152 Author chain L； PDBConstruct 1–151； UniProt 2–152 Author chain M； PDBConstruct 1–151； UniProt 2–152 Author chain N； PDBConstruct 1–151； UniProt 2–152 Author chain O； PDBConstruct 1–151； UniProt 2–152 Author chain P； PDBConstruct 1–151； UniProt 2–152

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	8iq0
Deposition date deposition_date	2023-03-15
Structure title title	Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized state
Keywords keywords	dimer, OXIDOREDUCTASE; OXIDOREDUCTASE
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	41.79 Å
Radius of gyration Rg (electron density) rg_electron	41.29 Å
Forward intensity I(0) i0	1025850000.00
Molecular weight molecular_weight	246770.0 kDa
Excluded volume excluded_volume	301890 Å³
Envelope volume envelope_volume	417400 Å³
Hydration-shell volume shell_volume	81512 Å³
Envelope diameter envelope_diameter	132.8 Å
Shell Rg shell_rg	49.19 Å
Envelope Rg envelope_rg	39.98 Å
Shape Rg shape_rg	41.31 Å
Total Rg total_rg	41.59 Å
Total atoms total_atoms	17219
Residues n_residues	2401
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	128.4 Å
Rg (real space) rg_real	41.53 Å
Rg uncertainty (real space) rg_real_error	0.85 Å
I(0) (real space) i0_real	1.0260e+09
I(0) uncertainty (real space) i0_real_error	1.7370e+07
Rg (reciprocal space) rg_reciprocal	41.79 Å
I(0) (reciprocal space) i0_reciprocal	1026000000.0000
Solution quality estimate total_estimate	0.8880
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	50.7 Å
Skewness Skewness skewness	0.064
Kurtosis Kurtosis kurtosis	-0.469
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	47660000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.881

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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	Superoxide dismutase [Cu-Zn]
Molecular weight formula_weight	15573.3 kDa
EC 编号 ec_number	1.15.1.1
Source method src_method	nat
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Atom count atom_count	18883

ATKAVCVLKGDGPVQGTIHFEAKGDTVVVTGSITGLTEGDHGFHVHQFGDNTQGCTSAGPHFNPLSKKHGGPKDEERHVGDLGNVTADKNGVAIVDIVDPLISLSGEYSIIGRTMVVHEKPDDLGRGGNEESTKTGNAGSRLACGVIGIAK

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	HYDROSULFURIC ACID
Molecular weight formula_weight	34.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1643

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7. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	8iq0A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0C01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0D01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0E01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0F01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0G01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0I01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0J01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0K01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0M01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0N01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0O01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	8iq0P01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

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8. Citations (1)

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Unit-cell length a length_a	74.348 Å
Unit-cell length b length_b	91.474 Å
Unit-cell length c length_c	91.164 Å
Unit-cell angle α angle_alpha	85.00 °
Unit-cell angle β angle_beta	78.06 °
Unit-cell angle γ angle_gamma	66.76 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	1.880 Å
Low-resolution limit resolution_low	30.680 Å
R factor r_factor	0.2031
R_work r_work	0.2009
R_free r_free	0.2445

fit	/app/data/saxs_computation/iq/8iq0/8iq0.fit
pddf	/app/data/pr_computation/iq/8iq0/8iq0.pr.out
profile	/app/data/saxs_computation/iq/8iq0/8iq0.dat