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8iq1

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

Method: X-RAY DIFFRACTION Dmax: 119.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Superoxide dismutase [Cu-Zn]

OrganismNot specified

UniProt P00442

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 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
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 × 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
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 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
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 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

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 8IQ1 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 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 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 ligand/ion 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 ligand/ion 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 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 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 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 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 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 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 ligand/ion 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 ligand/ion 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 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 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 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 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 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 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 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 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 ligand/ion 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 ligand/ion 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
8IQ0 Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized 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 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
8IQ0 Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized 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 × 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
8IQ0 Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized 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 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
8IQ0 Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized 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 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
8IQ0 Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized state Deposited 2023-03-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain I 2–152（151 aa）
Chain J 2–152（151 aa）
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
8IQ0 Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized state Deposited 2023-03-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain K 2–152（151 aa）
Chain L 2–152（151 aa）
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
8IQ0 Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized state Deposited 2023-03-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain M 2–152（151 aa）
Chain N 2–152（151 aa）
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
8IQ0 Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized state Deposited 2023-03-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain O 2–152（151 aa）
Chain P 2–152（151 aa）
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

24 other PDB entries and 35 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

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

SAXS profile for 8iq1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8iq1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8iq1
Deposition date deposition_date2023-03-15
Structure title titleCrystal structure of hydrogen sulfide-bound superoxide dismutase in reduced state
Keywords keywordsdimer, oxidoreductase; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.03 Å
Radius of gyration Rg (electron density) rg_electron35.36 Å
Forward intensity I(0) i0277888000.00
Molecular weight molecular_weight124920.0 kDa
Excluded volume excluded_volume152360 ų
Envelope volume envelope_volume204060 ų
Hydration-shell volume shell_volume48441 ų
Envelope diameter envelope_diameter129.7 Å
Shell Rg shell_rg41.48 Å
Envelope Rg envelope_rg34.73 Å
Shape Rg shape_rg35.38 Å
Total Rg total_rg35.72 Å
Total atoms total_atoms8700
Residues n_residues1205
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax119.7 Å
Rg (real space) rg_real35.96 Å
Rg uncertainty (real space) rg_real_error0.87 Å
I(0) (real space) i0_real2.7790e+08
I(0) uncertainty (real space) i0_real_error4.4670e+06
Rg (reciprocal space) rg_reciprocal36.01 Å
I(0) (reciprocal space) i0_reciprocal277900000.0000
Solution quality estimate total_estimate0.8629
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary49.0 Å
Skewness Skewness skewness0.263
Kurtosis Kurtosis kurtosis-0.239
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha24890000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.758; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.937
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id8iq1A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily200 — Superoxide dismutase, copper/zinc binding domain
Domain ID domain_id8iq1B01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily200 — Superoxide dismutase, copper/zinc binding domain
Domain ID domain_id8iq1C01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily200 — Superoxide dismutase, copper/zinc binding domain
Domain ID domain_id8iq1D01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily200 — Superoxide dismutase, copper/zinc binding domain
Domain ID domain_id8iq1E01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily200 — Superoxide dismutase, copper/zinc binding domain
Domain ID domain_id8iq1F01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily200 — Superoxide dismutase, copper/zinc binding domain
Domain ID domain_id8iq1G01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily200 — Superoxide dismutase, copper/zinc binding domain
Domain ID domain_id8iq1H01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily200 — Superoxide dismutase, copper/zinc binding domain
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8. Citations (1)

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9. Files and Curves (10)