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- PDB-1zte: Contribution to Structure and Catalysis of Tyrosine 34 in Human M... -

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Basic information

Entry
Database: PDB / ID: 1zte
TitleContribution to Structure and Catalysis of Tyrosine 34 in Human Manganese Suerpoxide Dismutase
ComponentsSuperoxide dismutase [Mn], mitochondrial
KeywordsOXIDOREDUCTASE / MNSOD / MANGANESE SUPEROXIDE DISMUTASE / Y34H MUTATION
Function / homology
Function and homology information


acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / erythrophore differentiation / positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / negative regulation of membrane hyperpolarization / detection of oxygen / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / response to silicon dioxide / response to L-ascorbic acid / response to isolation stress ...acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / erythrophore differentiation / positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / negative regulation of membrane hyperpolarization / detection of oxygen / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / response to silicon dioxide / response to L-ascorbic acid / response to isolation stress / intracellular oxygen homeostasis / response to selenium ion / response to superoxide / cellular response to ethanol / superoxide anion generation / hydrogen peroxide biosynthetic process / response to manganese ion / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of vascular associated smooth muscle cell apoptotic process / response to zinc ion / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / superoxide metabolic process / negative regulation of fat cell differentiation / superoxide dismutase / Detoxification of Reactive Oxygen Species / mitochondrial nucleoid / superoxide dismutase activity / negative regulation of vascular associated smooth muscle cell proliferation / hemopoiesis / response to immobilization stress / response to axon injury / response to hyperoxia / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / neuron development / response to cadmium ion / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to electrical stimulus / negative regulation of fibroblast proliferation / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / respiratory electron transport chain / release of cytochrome c from mitochondria / post-embryonic development / liver development / regulation of mitochondrial membrane potential / response to activity / locomotory behavior / response to gamma radiation / Transcriptional activation of mitochondrial biogenesis / response to hydrogen peroxide / oxygen binding / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of nitric oxide biosynthetic process / manganese ion binding / heart development / cellular response to oxidative stress / protein homotetramerization / negative regulation of neuron apoptotic process / response to lipopolysaccharide / response to hypoxia / positive regulation of cell migration / mitochondrial matrix / response to xenobiotic stimulus / negative regulation of cell population proliferation / regulation of transcription by RNA polymerase II / enzyme binding / mitochondrion / DNA binding / extracellular exosome / identical protein binding
Similarity search - Function
: / Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain ...: / Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Superoxide dismutase [Mn], mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHearn, A.S. / Perry, J.J. / Cabelii, D.E. / Tainer, J.A. / Nick, H.S. / Silverman, D.S.
CitationJournal: Biochemistry / Year: 2009
Title: Contribution of human manganese superoxide dismutase tyrosine 34 to structure and catalysis.
Authors: Perry, J.J. / Hearn, A.S. / Cabelli, D.E. / Nick, H.S. / Tainer, J.A. / Silverman, D.N.
History
DepositionMay 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 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_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_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 1.4Aug 23, 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 [Mn], mitochondrial
B: Superoxide dismutase [Mn], mitochondrial
C: Superoxide dismutase [Mn], mitochondrial
D: Superoxide dismutase [Mn], mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0528
Polymers88,8324
Non-polymers2204
Water19,9791109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8430 Å2
ΔGint-43 kcal/mol
Surface area31260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.665, 77.837, 136.222
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a tetramer

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Components

#1: Protein
Superoxide dismutase [Mn], mitochondrial


Mass: 22208.086 Da / Num. of mol.: 4 / Mutation: Y34H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD2 / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / Strain (production host): QC774I (SOD--) / References: UniProt: P04179, superoxide dismutase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1109 / 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: 2.88 Å3/Da / Density % sol: 57.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.8
Details: 25mM K2HPO4, 22% poly(ethylene glycol) (PEG) 2000 monomethyl ether, pH 7.8, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.95 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.85→37.4 Å / Num. all: 67566 / Num. obs: 61782 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 15.2
Reflection shellResolution: 1.85→1.97 Å / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 3 / % possible all: 82.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N0J.pdb

1n0j


Resolution: 1.85→37.4 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 559703.04 / Data cutoff low absF: 0 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.245 3133 5.1 %RANDOM
Rwork0.206 ---
obs0.206 61782 91.4 %-
all-67566 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.325 Å2 / ksol: 0.335855 e/Å3
Displacement parametersBiso mean: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å20 Å20 Å2
2--5.41 Å20 Å2
3----3.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.85→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6284 0 8 1105 7397
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it2.942.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 437 5 %
Rwork0.252 8246 -
obs--78.3 %

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