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- PDB-3sod: CHANGES IN CRYSTALLOGRAPHIC STRUCTURE AND THERMOSTABILITY OF A CU... -

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Basic information

Entry
Database: PDB / ID: 3sod
TitleCHANGES IN CRYSTALLOGRAPHIC STRUCTURE AND THERMOSTABILITY OF A CU,ZN SUPEROXIDE DISMUTASE MUTANT RESULTING FROM THE REMOVAL OF BURIED CYSTEINE
ComponentsCOPPER,ZINC SUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE (SUPEROXIDE ACCEPTOR)
Function / homology
Function and homology information


Platelet degranulation / Detoxification of Reactive Oxygen Species / positive regulation of catalytic activity / neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization ...Platelet degranulation / Detoxification of Reactive Oxygen Species / positive regulation of catalytic activity / neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / myeloid cell homeostasis / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / superoxide dismutase activity / transmission of nerve impulse / regulation of multicellular organism growth / response to axon injury / ovarian follicle development / glutathione metabolic process / embryo implantation / dendrite cytoplasm / removal of superoxide radicals / reactive oxygen species metabolic process / positive regulation of cytokine production / regulation of mitochondrial membrane potential / locomotory behavior / response to hydrogen peroxide / sensory perception of sound / regulation of blood pressure / protein polyubiquitination / ubiquitin-protein transferase activity / peroxisome / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / response to ethanol / spermatogenesis / negative regulation of neuron apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / intracellular iron ion homeostasis / positive regulation of MAPK cascade / copper ion binding / neuronal cell body / protein homodimerization activity / protein-containing complex / mitochondrion / zinc ion binding / nucleus / cytosol / cytoplasm
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: 2.1 Å
AuthorsMcree, D.E. / Redford, S.M. / Getzoff, E.D. / Lepock, J.R. / Hallewell, R.A. / Tainer, J.A.
CitationJournal: J.Biol.Chem. / Year: 1990
Title: Changes in crystallographic structure and thermostability of a Cu,Zn superoxide dismutase mutant resulting from the removal of a buried cysteine.
Authors: McRee, D.E. / Redford, S.M. / Getzoff, E.D. / Lepock, J.R. / Hallewell, R.A. / Tainer, J.A.
History
DepositionJun 26, 1990Processing site: BNL
Revision 1.0Apr 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,78512
Polymers62,2694
Non-polymers5168
Water00
1
O: COPPER,ZINC SUPEROXIDE DISMUTASE
Y: COPPER,ZINC SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3936
Polymers31,1352
Non-polymers2584
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: COPPER,ZINC SUPEROXIDE DISMUTASE
B: COPPER,ZINC SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3936
Polymers31,1352
Non-polymers2584
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.500, 89.400, 70.500
Angle α, β, γ (deg.)90.00, 95.70, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.8754, 0.1098, -0.4707), (0.1633, -0.8494, -0.5018), (-0.455, -0.5162, 0.7257)-60.022, 30.766, -6.904
2given(0.9558, 0.0244, -0.2931), (-0.0256, -0.9858, -0.1658), (-0.293, 0.166, -0.9416)2.998, 32.29, -2.7
3given(-0.7631, 0.2347, -0.6022), (-0.0343, 0.9157, 0.4004), (0.6454, 0.3262, -0.6907)-52.144, 5.647, 23.811

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Components

#1: Protein
COPPER,ZINC SUPEROXIDE DISMUTASE


Mass: 15567.311 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
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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal grow
*PLUS
pH: 6.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
149 %(v/v)MPD11
230 mMpotassium phosphate11
30.5 %antibiotic-antimycotic11
410 mg/mlprotein11

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Data collection

Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 28705 / % possible obs: 82 % / Num. measured all: 60573 / Rmerge(I) obs: 0.099
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % possible obs: 68 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.19 / Highest resolution: 2.1 Å
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 0 8 0 4384
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.03
X-RAY DIFFRACTIONx_angle_deg4
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / Num. reflection obs: 23715 / σ(I): 3 / Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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