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- PDB-5j07: Monomeric Human Cu,Zn Superoxide dismutase, loops IV and VII dele... -

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Basic information

Entry
Database: PDB / ID: 5j07
TitleMonomeric Human Cu,Zn Superoxide dismutase, loops IV and VII deleted, apo form, circular permutant P1/2
ComponentsSuperoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / SOD1
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / 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 / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus ...action potential initiation / neurofilament cytoskeleton organization / 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 / anterograde axonal transport / 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 / retrograde axonal transport / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / superoxide dismutase / positive regulation of catalytic activity / 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 / neuronal action potential / ectopic germ cell programmed cell death / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / glutathione metabolic process / reactive oxygen species metabolic process / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / : / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / locomotory behavior / positive regulation of cytokine production / determination of adult lifespan / placenta development / 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 / protein-folding chaperone binding / response to heat / 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
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, H. / Lang, L. / Logan, D. / Danielsson, J. / Oliveberg, M.
CitationJournal: J. Am. Chem. Soc. / Year: 2016
Title: Tricking a Protein To Swap Strands.
Authors: Wang, H. / Lang, L. / Logan, D.T. / Danielsson, J. / Oliveberg, M.
History
DepositionMar 27, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)22,6352
Polymers22,6352
Non-polymers00
Water1,53185
1
A: Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)11,3181
Polymers11,3181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)11,3181
Polymers11,3181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.040, 75.040, 59.010
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 11317.631 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P00441, superoxide dismutase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5 / Details: 0.1 M MIB buffer pH 5.0 25 % w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 12893 / % possible obs: 100 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 15.2
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.618

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bcz

4bcz


Resolution: 2→32.51 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 15.047 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.174
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 644 5 %RANDOM
Rwork0.1927 ---
obs0.1946 12221 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 130.04 Å2 / Biso mean: 49.806 Å2 / Biso min: 20.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20.96 Å20 Å2
2--0.96 Å20 Å2
3----3.11 Å2
Refinement stepCycle: final / Resolution: 2→32.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1595 0 0 85 1680
Biso mean---52.33 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0191615
X-RAY DIFFRACTIONr_bond_other_d0.0010.021582
X-RAY DIFFRACTIONr_angle_refined_deg0.881.9442182
X-RAY DIFFRACTIONr_angle_other_deg0.80133638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7555228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77125.71456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.25315252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.748154
X-RAY DIFFRACTIONr_chiral_restr0.0560.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021904
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02336
X-RAY DIFFRACTIONr_mcbond_it3.1744.119918
X-RAY DIFFRACTIONr_mcbond_other3.1694.111917
X-RAY DIFFRACTIONr_mcangle_it4.1126.1551144
X-RAY DIFFRACTIONr_rigid_bond_restr7.11333197
X-RAY DIFFRACTIONr_sphericity_free49.725536
X-RAY DIFFRACTIONr_sphericity_bonded32.34153226
LS refinement shellResolution: 2.001→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 45 -
Rwork0.206 896 -
all-941 -
obs--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)
10.1297-0.0288-0.06580.17620.08130.10550.0203-0.0301-0.0115-0.0426-0.0201-0.02280.02190.0004-0.00010.06340.0039-0.00550.03620.00770.148520.6882-18.2236-0.1497
20.56860.377-0.14510.5358-0.24580.1174-0.08070.0211-0.0923-0.0710.0427-0.06080.0228-0.01390.0380.0523-0.00260.01080.052-0.01290.161324.2713-12.6403-22.2038
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 115
2X-RAY DIFFRACTION2B1 - 115

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