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- PDB-2gbt: C6A/C111A CuZn Superoxide dismutase -

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Basic information

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


action potential initiation / neurofilament cytoskeleton organization / anterograde axonal transport / retrograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / anterograde axonal transport / retrograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / superoxide anion generation / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / positive regulation of catalytic activity / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / neuronal action potential / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / glutathione metabolic process / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / embryo implantation / reactive oxygen species metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / positive regulation of superoxide anion generation / regulation of mitochondrial membrane potential / thymus development / locomotory behavior / placenta development / response to organic substance / determination of adult lifespan / positive regulation of cytokine production / sensory perception of sound / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / gene expression / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / copper ion binding / neuronal cell body / apoptotic process / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / 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: 1.7 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 1.3May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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

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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3128
Polymers63,0544
Non-polymers2584
Water9,674537
1
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7856
Polymers31,5272
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-11 kcal/mol
Surface area14230 Å2
MethodPISA
2
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)31,5272
Polymers31,5272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-11 kcal/mol
Surface area12120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.618, 35.257, 114.971
Angle α, β, γ (deg.)90.00, 112.17, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-273-

HOH

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Components

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


Mass: 15763.430 Da / Num. of mol.: 4 / Mutation: C6A/C111A
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 / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% PEG8000, 50mM TRIS-HCL, 50mM NaAc, 1mM EDTA, 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: 1.092 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 20, 2004
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.092 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 64389 / Num. obs: 64389 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.059
Reflection shellResolution: 1.7→1.79 Å / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1HL4

1hl4


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.979 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3249 5.1 %RANDOM
Rwork0.203 ---
all0.204 64389 --
obs0.204 64189 98.94 %-
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: 31.885 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å20 Å2-0.73 Å2
2--2.16 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4026 0 4 537 4567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0214094
X-RAY DIFFRACTIONr_bond_other_d0.0020.023650
X-RAY DIFFRACTIONr_angle_refined_deg1.0311.9415532
X-RAY DIFFRACTIONr_angle_other_deg0.67338533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6875546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78925.491173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.40415657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3241514
X-RAY DIFFRACTIONr_chiral_restr0.0620.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02744
X-RAY DIFFRACTIONr_nbd_refined0.1810.2637
X-RAY DIFFRACTIONr_nbd_other0.1710.23563
X-RAY DIFFRACTIONr_nbtor_refined0.1560.21962
X-RAY DIFFRACTIONr_nbtor_other0.0790.22344
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2438
X-RAY DIFFRACTIONr_metal_ion_refined0.1740.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.080.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1820.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.214
X-RAY DIFFRACTIONr_mcbond_it0.5691.53547
X-RAY DIFFRACTIONr_mcbond_other0.091.51184
X-RAY DIFFRACTIONr_mcangle_it0.67724289
X-RAY DIFFRACTIONr_scbond_it1.20131678
X-RAY DIFFRACTIONr_scangle_it1.6044.51243
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 235 -
Rwork0.291 4458 -
obs-4693 99.15 %
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)
12.28930.18411.21491.53620.20094.68420.0610.1605-0.1477-0.0523-0.082-0.050.1859-0.28440.021-0.2331-0.06820.0042-0.040.0059-0.2186-13.0429-2.899220.8128
22.28680.02070.10021.27580.13893.67760.0247-0.33950.01310.14570.0641-0.00420.1141-0.0202-0.0888-0.2364-0.0204-0.0023-0.00330.0104-0.222-3.75383.088746.3614
34.05330.3474-0.08471.3111-0.01124.51780.0669-0.39930.2244-0.01390.01910.0109-0.20110.1988-0.086-0.2413-0.0402-0.0042-0.1314-0.0127-0.214829.15711.811230.512
42.8302-0.04650.37662.20320.13225.64110.01620.45-0.0564-0.1130.00130.01690.09030.0209-0.0175-0.1985-0.0352-0.0102-0.14290.0166-0.215723.05015.04228.3858
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 1532 - 153
22BB2 - 1532 - 153
33CC1 - 1531 - 153
44DD2 - 1532 - 153

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