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- PDB-1sos: ATOMIC STRUCTURES OF WILD-TYPE AND THERMOSTABLE MUTANT RECOMBINAN... -

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Entry
Database: PDB / ID: 1sos
TitleATOMIC STRUCTURES OF WILD-TYPE AND THERMOSTABLE MUTANT RECOMBINANT HUMAN CU, ZN SUPEROXIDE DISMUTASE
ComponentsSUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE (SUPEROXIDE ACCEPTOR)
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / retrograde axonal transport / superoxide anion generation / regulation of GTPase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / superoxide metabolic process / heart contraction / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / neuronal action potential / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / dendrite cytoplasm / embryo implantation / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / thymus development / positive regulation of superoxide anion generation / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / placenta development / sensory perception of sound / response to hydrogen peroxide / small GTPase binding / mitochondrial intermembrane space / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / gene expression / spermatogenesis / negative regulation of neuron apoptotic process / response to ethanol / intracellular iron ion homeostasis / positive regulation of MAPK cascade / mitochondrial matrix / positive regulation of apoptotic process / copper ion binding / response to xenobiotic stimulus / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsParge, H.E. / Hallewell, R.A. / Tainer, J.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Atomic structures of wild-type and thermostable mutant recombinant human Cu,Zn superoxide dismutase.
Authors: Parge, H.E. / Hallewell, R.A. / Tainer, J.A.
History
DepositionFeb 11, 1992Processing 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 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 6, 2024Group: 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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
Remark 700SHEET THE SHEETS PRESENTED ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA-BARRELS. EACH ...SHEET THE SHEETS PRESENTED ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA-BARRELS. EACH ONE IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUPEROXIDE DISMUTASE
F: SUPEROXIDE DISMUTASE
B: SUPEROXIDE DISMUTASE
G: SUPEROXIDE DISMUTASE
C: SUPEROXIDE DISMUTASE
H: SUPEROXIDE DISMUTASE
D: SUPEROXIDE DISMUTASE
I: SUPEROXIDE DISMUTASE
E: SUPEROXIDE DISMUTASE
J: SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,53632
Polymers158,05510
Non-polymers1,48222
Water8,989499
1
A: SUPEROXIDE DISMUTASE
F: SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9657
Polymers31,6112
Non-polymers3545
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-37 kcal/mol
Surface area13630 Å2
MethodPISA
2
B: SUPEROXIDE DISMUTASE
G: SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8696
Polymers31,6112
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-44 kcal/mol
Surface area13750 Å2
MethodPISA
3
C: SUPEROXIDE DISMUTASE
H: SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8696
Polymers31,6112
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-39 kcal/mol
Surface area13830 Å2
MethodPISA
4
D: SUPEROXIDE DISMUTASE
I: SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9657
Polymers31,6112
Non-polymers3545
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-47 kcal/mol
Surface area13680 Å2
MethodPISA
5
E: SUPEROXIDE DISMUTASE
J: SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8696
Polymers31,6112
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-37 kcal/mol
Surface area13620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.200, 167.000, 145.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9827, 0.008, 0.185), (0.0182, -0.9901, 0.1394), (0.1843, 0.1403, 0.9728)120.63, 56.458, -15.304
2given(-0.4637, -0.8858, 0.0151), (0.886, -0.4637, 0.0082), (-0.0002, 0.0172, 0.9999)106.406, -66.096, 0.017
3given(0.467, 0.8674, 0.1719), (-0.8837, 0.4509, 0.1257), (0.0315, -0.2106, 0.9771)15.104, 123.625, -4.286
4given(-0.5349, 0.8427, 0.0608), (-0.8444, -0.5357, -0.0032), (0.0299, -0.053, 0.9981)111.294, 61, -3.262
5given(0.5227, -0.8385, 0.1541), (0.8329, 0.5408, 0.1176), (-0.1819, 0.0669, 0.981)10.876, -2.131, 11.151
6given(-0.981, -0.0269, -0.1923), (0.0282, -0.9996, -0.004), (-0.1922, -0.0094, 0.9813)208.836, 28.442, 29.487
7given(0.9361, 0.0076, 0.3515), (-0.0569, 0.9899, 0.1301), (-0.347, -0.1419, 0.9271)-79.86, 33.912, 53.157
8given(0.4766, 0.879, 0.0103), (-0.8779, 0.4766, -0.0466), (-0.0458, 0.0132, 0.9989)-19.714, 102.413, 9.159
9given(-0.4753, -0.8659, 0.1556), (0.876, -0.4494, 0.1752), (-0.0818, 0.2196, 0.9722)142.207, -44.744, 5.365

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Components

#1: Protein
SUPEROXIDE DISMUTASE


Mass: 15805.468 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00441, superoxide dismutase
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O
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: 3.94 Å3/Da / Density % sol: 68.8 %
Crystal grow
*PLUS
pH: 7.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMpotassium phosphate1drop
22 %(w/v)protein1drop
350 mMTris-HCl1reservoir
450 mM1reservoirNaCl
50.1 mMEDTA1reservoir
60.01 %1reservoirNaN3

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Data collection

Reflection
*PLUS
Highest resolution: 2.48 Å / Num. obs: 77344 / % possible obs: 88.4 % / Num. measured all: 742579

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.202 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11120 0 30 499 11649
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg3.5
Software
*PLUS
Name: XPLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 63790 / σ(F): 3 / Rfactor Rwork: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.5

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