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- PDB-4mcm: Human SOD1 C57S Mutant, As-isolated -

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Basic information

Entry
Database: PDB / ID: 4mcm
TitleHuman SOD1 C57S Mutant, As-isolated
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / HUMAN CU / ZN SUPEROXIDE DISMUTASE / ANTIOXIDANT / METAL-BINDING / AMYOTROPHIC LATERAL SCLEROSIS / DISULFIDE BOND
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
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSea, K. / Sohn, S.H. / Durazo, A. / Sheng, Y. / Shaw, B. / Cao, X. / Taylor, A.B. / Whitson, L.J. / Holloway, S.P. / Hart, P.J. ...Sea, K. / Sohn, S.H. / Durazo, A. / Sheng, Y. / Shaw, B. / Cao, X. / Taylor, A.B. / Whitson, L.J. / Holloway, S.P. / Hart, P.J. / Cabelli, D.E. / Gralla, E.B. / Valentine, J.S.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Insights into the role of the unusual disulfide bond in copper-zinc superoxide dismutase.
Authors: Sea, K. / Sohn, S.H. / Durazo, A. / Sheng, Y. / Shaw, B.F. / Cao, X. / Taylor, A.B. / Whitson, L.J. / Holloway, S.P. / Hart, P.J. / Cabelli, D.E. / Gralla, E.B. / Valentine, J.S.
History
DepositionAug 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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.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_ref_seq_dif.details / _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
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
I: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
K: Superoxide dismutase [Cu-Zn]
L: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,65350
Polymers189,73812
Non-polymers2,91538
Water19,7081094
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1739
Polymers31,6232
Non-polymers5507
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-140 kcal/mol
Surface area13800 Å2
MethodPISA
2
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0778
Polymers31,6232
Non-polymers4546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-103 kcal/mol
Surface area13960 Å2
MethodPISA
3
E: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0778
Polymers31,6232
Non-polymers4546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-132 kcal/mol
Surface area13840 Å2
MethodPISA
4
G: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1739
Polymers31,6232
Non-polymers5507
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-135 kcal/mol
Surface area14000 Å2
MethodPISA
5
I: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0778
Polymers31,6232
Non-polymers4546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-78 kcal/mol
Surface area14030 Å2
MethodPISA
6
K: Superoxide dismutase [Cu-Zn]
L: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0778
Polymers31,6232
Non-polymers4546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-115 kcal/mol
Surface area13910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.530, 163.883, 174.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Superoxide dismutase [Cu-Zn] / Superoxide dismutase 1 / hSod1


Mass: 15811.496 Da / Num. of mol.: 12 / Fragment: UNP residues 2-154 / Mutation: C57S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: YEP351-HSOD / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P00441, superoxide dismutase
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1094 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M ammonium sulfate, 0.1 M bis-tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0332 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 108701 / % possible obs: 99.3 % / Redundancy: 6.1 % / Biso Wilson estimate: 32.9 Å2 / Rsym value: 0.064 / Net I/σ(I): 25.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 10297 / Rsym value: 0.482 / % possible all: 95.3

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AZV

1azv


Resolution: 2.2→29.836 Å / SU ML: 0.3 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2621 5325 4.98 %random
Rwork0.2105 ---
obs0.213 106830 98.18 %-
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13310 0 94 1094 14498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813588
X-RAY DIFFRACTIONf_angle_d1.15418344
X-RAY DIFFRACTIONf_dihedral_angle_d13.9154862
X-RAY DIFFRACTIONf_chiral_restr0.0742015
X-RAY DIFFRACTIONf_plane_restr0.0042472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.35511570.28072982X-RAY DIFFRACTION88
2.225-2.25120.32621510.27033128X-RAY DIFFRACTION91
2.2512-2.27860.32491570.26733145X-RAY DIFFRACTION93
2.2786-2.30740.321710.25943209X-RAY DIFFRACTION94
2.3074-2.33780.33361950.25423243X-RAY DIFFRACTION96
2.3378-2.36980.30371440.25233279X-RAY DIFFRACTION96
2.3698-2.40360.28361650.25063344X-RAY DIFFRACTION97
2.4036-2.43950.33241590.25313290X-RAY DIFFRACTION97
2.4395-2.47760.28551920.25523359X-RAY DIFFRACTION98
2.4776-2.51820.29031700.2563388X-RAY DIFFRACTION99
2.5182-2.56160.36852070.25543368X-RAY DIFFRACTION99
2.5616-2.60820.29932100.24033328X-RAY DIFFRACTION99
2.6082-2.65830.35291710.24883435X-RAY DIFFRACTION100
2.6583-2.71250.32261840.24463356X-RAY DIFFRACTION99
2.7125-2.77150.28311800.23723457X-RAY DIFFRACTION100
2.7715-2.83590.29281860.23733394X-RAY DIFFRACTION100
2.8359-2.90670.32271730.24713436X-RAY DIFFRACTION100
2.9067-2.98530.26031760.23433463X-RAY DIFFRACTION100
2.9853-3.0730.3061760.23583410X-RAY DIFFRACTION100
3.073-3.17210.2941780.22263438X-RAY DIFFRACTION100
3.1721-3.28530.27472080.21193431X-RAY DIFFRACTION100
3.2853-3.41670.26991840.21053450X-RAY DIFFRACTION100
3.4167-3.5720.25872060.20893461X-RAY DIFFRACTION100
3.572-3.75990.24561630.19313442X-RAY DIFFRACTION100
3.7599-3.9950.22091860.18883471X-RAY DIFFRACTION100
3.995-4.30260.20781740.16833481X-RAY DIFFRACTION100
4.3026-4.73410.23341800.16113506X-RAY DIFFRACTION100
4.7341-5.41560.22661530.16423558X-RAY DIFFRACTION100
5.4156-6.80960.19581800.19013561X-RAY DIFFRACTION100
6.8096-29.83880.19661890.19183692X-RAY DIFFRACTION99

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