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- PDB-2gbv: C6A/C111A/C57A/C146A holo CuZn Superoxide dismutase -

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Basic information

Entry
Database: PDB / ID: 2gbv
TitleC6A/C111A/C57A/C146A holo CuZn Superoxide dismutase
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / HUMAN CU/ZN SUPEROXIDE DISMUTASE / CYSTEIN-FREE
Function / homology
Function and homology information


action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway ...action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / 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 / cellular response to potassium ion / retrograde axonal transport / superoxide anion generation / myeloid cell homeostasis / regulation of GTPase activity / response to copper ion / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / Detoxification of Reactive Oxygen Species / cellular response to ATP / superoxide dismutase activity / negative regulation of reproductive process / negative regulation of developmental process / transmission of nerve impulse / cellular response to cadmium ion / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / neuronal action potential / ovarian follicle development / positive regulation of superoxide anion generation / regulation of mitochondrial membrane potential / axon cytoplasm / glutathione metabolic process / embryo implantation / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / positive regulation of phagocytosis / placenta development / response to amphetamine / thymus development / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / response to nutrient levels / response to hydrogen peroxide / sensory perception of sound / regulation of blood pressure / mitochondrial intermembrane space / small GTPase binding / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / response to ethanol / spermatogenesis / gene expression / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / lysosome / positive regulation of MAPK cascade / positive regulation of apoptotic process / mitochondrial matrix / response to xenobiotic stimulus / copper ion binding / 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 (I) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsHornberg, A. / Logan, D.T. / Marklund, S.L. / Oliveberg, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Coupling between Disulphide Status, Metallation and Dimer Interface Strength in Cu/Zn Superoxide Dismutase
Authors: Hornberg, A. / Logan, D.T. / Marklund, S.L. / Oliveberg, M.
History
DepositionMar 11, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,28330
Polymers156,99310
Non-polymers1,29020
Water26,9861498
1
A: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6576
Polymers31,3992
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-12 kcal/mol
Surface area13920 Å2
MethodPISA
2
B: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6576
Polymers31,3992
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-12 kcal/mol
Surface area14090 Å2
MethodPISA
3
C: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6576
Polymers31,3992
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-10 kcal/mol
Surface area14130 Å2
MethodPISA
4
D: Superoxide dismutase [Cu-Zn]
I: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6576
Polymers31,3992
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-12 kcal/mol
Surface area14070 Å2
MethodPISA
5
E: Superoxide dismutase [Cu-Zn]
J: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6576
Polymers31,3992
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-11 kcal/mol
Surface area14230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.800, 202.370, 143.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-1591-

HOH

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Components

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


Mass: 15699.299 Da / Num. of mol.: 10 / Mutation: C6A/C111A/C57A/C146A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: pACA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: UniProt: P00441, superoxide dismutase
#2: Chemical
ChemComp-CU1 / COPPER (I) 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1498 / 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: 3.86 Å3/Da / Density % sol: 68.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.8M Ammonium Sulphate, 50mM NaAc, 0.1M TRIS-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 26, 2004
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 162729 / Num. obs: 162729 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.064
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 8.9 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
XDSdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1N18

1n18


Resolution: 2→19.88 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.274 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.207 8162 5 %RANDOM
Rwork0.183 ---
all0.184 162729 --
obs0.184 162695 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.336 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20 Å2
2---0.3 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11060 0 20 1498 12578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02111240
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210000
X-RAY DIFFRACTIONr_angle_refined_deg1.0551.94315180
X-RAY DIFFRACTIONr_angle_other_deg0.669323410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.951520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.48725.625480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.075151810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.1371540
X-RAY DIFFRACTIONr_chiral_restr0.0610.21680
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213030
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022040
X-RAY DIFFRACTIONr_nbd_refined0.1830.21891
X-RAY DIFFRACTIONr_nbd_other0.1730.210075
X-RAY DIFFRACTIONr_nbtor_refined0.1580.25430
X-RAY DIFFRACTIONr_nbtor_other0.0790.26409
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.21166
X-RAY DIFFRACTIONr_metal_ion_refined0.0920.236
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1110.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1950.2107
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.265
X-RAY DIFFRACTIONr_mcbond_it0.5191.59828
X-RAY DIFFRACTIONr_mcbond_other0.0741.53280
X-RAY DIFFRACTIONr_mcangle_it0.577211800
X-RAY DIFFRACTIONr_scbond_it1.10834580
X-RAY DIFFRACTIONr_scangle_it1.5014.53380
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 622 -
Rwork0.188 11236 -
obs-11858 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.87230.4257-0.36161.84050.19722.1567-0.0080.00740.01120.0505-0.01750.11810.1542-0.21720.0255-0.1565-0.09090.0307-0.1304-0.0263-0.1666123.768557.051452.805
21.79760.23521.18963.53280.33495.335-0.41820.05330.2497-0.0511-0.0118-0.0506-1.35730.26560.430.3769-0.0684-0.1771-0.17730.0096-0.0954174.8075117.669852.6607
31.9793-0.93860.13422.3628-0.22821.7240.0008-0.0094-0.0445-0.0402-0.02240.01590.00290.00120.0217-0.1930.05410.0139-0.15830.0128-0.1985203.167943.430652.7197
42.89060.28140.1632.98731.16322.58040.13940.2329-0.01880.0164-0.2443-0.1403-0.1348-0.08860.105-0.1727-0.0624-0.0612-0.02550.0295-0.122177.1731149.271252.3769
52.0663-0.06650.41774.812-1.05382.459-0.00110.1330.2743-0.43240.03790.21160.0659-0.1692-0.0368-0.06230.0006-0.0011-0.1301-0.02920.0592126.504587.215746.5566
63.06350.11290.17551.97230.49091.2139-0.0046-0.0009-0.05810.0088-0.04820.11450.1016-0.06540.0528-0.1754-0.03270.0252-0.1852-0.0187-0.2074149.622566.349153.6764
71.76740.83520.43162.5523-0.24411.8272-0.06820.06090.12450.0453-0.05960.0312-0.13140.07520.1278-0.17840.0088-0.0036-0.1932-0.0093-0.2036170.785390.553.7968
82.2027-1.3137-0.27783.34020.20391.4515-0.01240.02240.0222-0.1611-0.0448-0.00910.02820.01370.0573-0.18410.03570.0032-0.15670.0135-0.2066181.311360.01253.9721
92.35190.1238-0.24862.3420.20321.3321-0.10720.10490.10470.07810.178-0.2531-0.08650.2432-0.0709-0.18580.0054-0.0532-0.0371-0.052-0.138151.5285139.243551.8282
102.95290.8923-0.05824.15130.59321.1308-0.07990.0841-0.2938-0.08670.02770.29670.0834-0.06710.0522-0.11660.03970.0005-0.14570.0097-0.0561130.8894114.255348.9272
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 153 / Label seq-ID: 1 - 153

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB
33CC
44DD
55EE
66FF
77GG
88HH
99II
1010JJ

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