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- PDB-1sda: CRYSTAL STRUCTURE OF PEROXYNITRITE-MODIFIED BOVINE CU,ZN SUPEROXI... -

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Basic information

Entry
Database: PDB / ID: 1sda
TitleCRYSTAL STRUCTURE OF PEROXYNITRITE-MODIFIED BOVINE CU,ZN SUPEROXIDE DISMUTASE
ComponentsCOPPER,ZINC SUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE(COPPER)
Function / homology
Function and homology information


Platelet degranulation / Detoxification of Reactive Oxygen Species / positive regulation of catalytic activity / neurofilament cytoskeleton organization / relaxation of vascular associated smooth muscle / protein phosphatase 2B binding / response to superoxide / peripheral nervous system myelin maintenance / Oxidoreductases; Acting on a sulfur group of donors / retina homeostasis ...Platelet degranulation / Detoxification of Reactive Oxygen Species / positive regulation of catalytic activity / neurofilament cytoskeleton organization / relaxation of vascular associated smooth muscle / protein phosphatase 2B binding / response to superoxide / peripheral nervous system myelin maintenance / Oxidoreductases; Acting on a sulfur group of donors / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / myeloid cell homeostasis / superoxide metabolic process / superoxide dismutase / muscle cell cellular homeostasis / superoxide dismutase activity / heart contraction / transmission of nerve impulse / regulation of multicellular organism growth / response to axon injury / ovarian follicle development / removal of superoxide radicals / embryo implantation / reactive oxygen species metabolic process / dendrite cytoplasm / positive regulation of cytokine production / regulation of mitochondrial membrane potential / glutathione metabolic process / response to hydrogen peroxide / locomotory behavior / sensory perception of sound / regulation of blood pressure / protein polyubiquitination / ubiquitin-protein transferase activity / peroxisome / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / negative regulation of neuron apoptotic process / response to ethanol / intracellular iron ion homeostasis / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of MAPK cascade / copper ion binding / neuronal cell body / protein homodimerization activity / protein-containing complex / mitochondrion / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsSmith, C.D. / Carson, M. / Van Der Woerd, M. / Chen, J. / Ischiropoulos, H. / Beckman, J.S.
Citation
Journal: Arch.Biochem.Biophys. / Year: 1992
Title: Crystal structure of peroxynitrite-modified bovine Cu,Zn superoxide dismutase.
Authors: Smith, C.D. / Carson, M. / van der Woerd, M. / Chen, J. / Ischiropoulos, H. / Beckman, J.S.
#1: Journal: Arch.Biochem.Biophys. / Year: 1992
Title: Peroxynitrite-Mediated Tyrosine Nitration Catalyzed by Superoxide Dismutase
Authors: Ischiropoulos, H. / Zhu, L. / Chen, J. / Tsai, M. / Martin, J.C. / Smith, C.D. / Beckman, J.S.
#2: Journal: J.Mol.Biol. / Year: 1982
Title: Determination and Analysis of the 2 Angstroms Structure of Copper, Zinc Superoxide Dismutase
Authors: Tainer, J.A. / Getzoff, E.D. / Beem, K.M. / Richardson, J.S. / Richardson, D.C.
History
DepositionJan 13, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: COPPER,ZINC SUPEROXIDE DISMUTASE
Y: COPPER,ZINC SUPEROXIDE DISMUTASE
B: COPPER,ZINC SUPEROXIDE DISMUTASE
G: COPPER,ZINC SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,09312
Polymers62,5774
Non-polymers5168
Water724
1
O: COPPER,ZINC SUPEROXIDE DISMUTASE
Y: COPPER,ZINC SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5476
Polymers31,2892
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: COPPER,ZINC SUPEROXIDE DISMUTASE
G: COPPER,ZINC SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5476
Polymers31,2892
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-36 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.650, 90.330, 71.650
Angle α, β, γ (deg.)90.00, 95.10, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.77055, 0.208642, -0.602263), (0.1721, -0.841702, -0.51178), (-0.613705, -0.498002, 0.612666)-59.5583, 29.3583, -13.275
2given(-0.745544, -0.057921, 0.663934), (0.218365, 0.919994, 0.325466), (-0.629667, 0.387629, -0.673248)-53.2802, -0.0007, -22.6929
3given(0.992474, -0.027802, -0.11926), (-0.008276, -0.986888, 0.161193), (-0.122178, -0.158992, -0.979691)-2.7675, 32.112, 3.4231
DetailsTHE TRANSFORMATION WHICH WILL PLACE THE YELLOW MONOMER INTO BEST ALIGNMENT WITH THE ORANGE MONOMER IS GIVEN BY MTRIX 1 BELOW. THE TRANSFORMATION WHICH WILL PLACE THE BLUE MONOMER INTO BEST ALIGNMENT WITH THE ORANGE MONOMER IS GIVEN BY MTRIX 2 BELOW. THE TRANSFORMATION WHICH WILL PLACE THE GREEN MONOMER INTO BEST ALIGNMENT WITH THE ORANGE MONOMER IS GIVEN BY MTRIX 3 BELOW.

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Components

#1: Protein
COPPER,ZINC SUPEROXIDE DISMUTASE


Mass: 15644.371 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00442, superoxide dismutase
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Compound detailsEACH MONOMER CONTAINS AN ACETYL GROUP BLOCKING THE N-TERMINUS, 151 RESIDUES, ZN ION, CU ION AND A ...EACH MONOMER CONTAINS AN ACETYL GROUP BLOCKING THE N-TERMINUS, 151 RESIDUES, ZN ION, CU ION AND A WATER MOLECULE. THE DOMINANT STRUCTURAL FEATURE OF EACH MONOMER IS AN EIGHT-STRANDED ANTI-PARALLEL BETA-BARREL. THERE ARE, HOWEVER, NO HYDROGEN BONDS BETWEEN STRANDS 4 AND 5. THIS BARREL IS DESCRIBED IN SHEET RECORDS BELOW AS A NINE-STRANDED SHEET WITH IDENTICAL FIRST AND LAST STRANDS. STRAND 8 OF THIS SHEET IS BIFURCATED SO THAT THE SHEET IN EACH CHAIN IS ACTUALLY PRESENTED AS TWO SHEETS IN EACH CHAIN THAT DIFFER ONLY IN STRAND 8.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal grow
*PLUS
Temperature: 5 ℃ / pH: 7.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12-7 mg/mlprotein1drop
228 %MPD1drop
350 mMpotassium phosphate1drop
455 %(v/v)MPD1reservoir
550 mMpotassium phosphate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Rmerge(I) obs: 0.323

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.187 / Rfactor obs: 0.187 / Highest resolution: 2.5 Å
Details: COORDINATES IN THE A*BC ORTHOGONAL FRAME ARE PRESENTED BELOW FOR FOUR MONOMERS. ONE ENZYMATICALLY ACTIVE SOD DIMER COMPRISES MONOMERS ORANGE (CHAIN INDICATOR O) AND YELLOW (Y). ANOTHER DIMER ...Details: COORDINATES IN THE A*BC ORTHOGONAL FRAME ARE PRESENTED BELOW FOR FOUR MONOMERS. ONE ENZYMATICALLY ACTIVE SOD DIMER COMPRISES MONOMERS ORANGE (CHAIN INDICATOR O) AND YELLOW (Y). ANOTHER DIMER COMPRISES MONOMERS BLUE (B) AND GREEN (G). FOR THE ACTIVE SITE HISTIDINES, THE PLACEMENT OF HYDROGENS WAS AS FOLLOWS FOR X-PLOR REFINEMENT: HIS 46, 118 HAVE A HYDROGEN ON THE DELTA NITROGEN; HIS 44, 69, 78 HAVE A HYDROGEN ON THE EPSILON NITROGEN; AND HIS 61 IS NEGATIVELY CHARGED WITH NEITHER HYDROGEN.
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 0 20 4 4404
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.23
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 6 Å / Rfactor obs: 0.187 / Rfactor Rwork: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.23

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