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- PDB-4xcr: Monomeric Human Cu,Zn Superoxide dismutase, loops IV and VII dele... -

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Basic information

Entry
Database: PDB / ID: 4xcr
TitleMonomeric Human Cu,Zn Superoxide dismutase, loops IV and VII deleted, apo form, mutant I35A
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / 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 ...action potential initiation / neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / 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 / superoxide anion generation / regulation of T cell differentiation in thymus / retina homeostasis / 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 / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / reactive oxygen species metabolic process / dendrite cytoplasm / removal of superoxide radicals / positive regulation of superoxide anion generation / thymus development / locomotory behavior / regulation of mitochondrial membrane potential / 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 / negative regulation of inflammatory response / regulation of blood pressure / peroxisome / Platelet degranulation / gene expression / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / response to ethanol / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / 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 / molecular replacement / Resolution: 3.602 Å
AuthorsWang, H. / Logan, D.T. / Danielsson, J. / Mu, X. / Binolfi, A. / Theillet, F. / Bekei, B. / Lang, L. / Wennerstrom, H. / Selenko, P. / Oliveberg, M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2015
Title: Thermodynamics of protein destabilization in live cells.
Authors: Danielsson, J. / Mu, X. / Lang, L. / Wang, H. / Binolfi, A. / Theillet, F.X. / Bekei, B. / Logan, D.T. / Selenko, P. / Wennerstrom, H. / Oliveberg, M.
History
DepositionDec 18, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Jan 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,8962
Polymers21,8962
Non-polymers00
Water0
1
A: Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)10,9481
Polymers10,9481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)10,9481
Polymers10,9481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.820, 70.820, 70.010
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 1 / hSod1


Mass: 10948.210 Da / Num. of mol.: 2 / Mutation: I45A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00441, superoxide dismutase

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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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.5 / Details: 0.1 M Bis Tris and 2.0 M ammonium sulfate / PH range: 5.5

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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: Nov 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.791
11K, H, -L20.209
ReflectionResolution: 3.6→46.13 Å / Num. obs: 2203 / % possible obs: 92.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.326 / Net I/σ(I): 2.3
Reflection shellResolution: 3.6→3.94 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 1.8 / Num. measured obs: 2754 / Num. unique all: 533 / % possible all: 93.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation35.41 Å3.61 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREP11.0.05phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BCZ

4bcz


Resolution: 3.602→46.133 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 219 9.97 %RANDOM
Rwork0.1853 1978 --
obs0.1906 2197 93.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.62 Å2 / Biso mean: 58.2323 Å2 / Biso min: 42.38 Å2
Refinement stepCycle: final / Resolution: 3.602→46.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1542 0 0 0 1542
Num. residues----220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041562
X-RAY DIFFRACTIONf_angle_d0.782110
X-RAY DIFFRACTIONf_chiral_restr0.033244
X-RAY DIFFRACTIONf_plane_restr0.002280
X-RAY DIFFRACTIONf_dihedral_angle_d14.062540
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6021-4.53760.23551100.1889995110594
4.5376-46.13680.24241090.1823983109292
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)
12.2874-2.0981.61253.44210.326.61290.0681-0.5034-0.38380.5120.2448-0.2006-0.13780.0019-00.6868-0.0279-0.01310.41320.04570.5507-18.6865-17.836411.8354
24.9135-1.7663-0.12764.1673-1.66834.9130.13140.8660.3175-0.4676-0.08030.42360.48010.0226-0.00020.4730.0678-0.09530.825-0.08430.6126-16.0756-21.9857-12.0035
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 110
2X-RAY DIFFRACTION2chain BB1 - 110

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