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- PDB-2adp: Nitrated Human Manganese Superoxide Dismutase -

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Basic information

Entry
Database: PDB / ID: 2adp
TitleNitrated Human Manganese Superoxide Dismutase
ComponentsSuperoxide dismutase [Mn]
KeywordsOXIDOREDUCTASE
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 / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / superoxide metabolic process / negative regulation of fat cell differentiation / response to zinc ion / 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 / neuron development / response to hyperoxia / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to cadmium ion / response to electrical stimulus / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / glutathione metabolic process / respiratory electron transport chain / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / release of cytochrome c from mitochondria / post-embryonic development / regulation of mitochondrial membrane potential / liver development / locomotory behavior / response to activity / 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 / positive regulation of nitric oxide biosynthetic process / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to oxidative stress / heart development / manganese ion binding / 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 / Manganese/iron superoxide dismutase, C-terminal ...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 / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsQuint, P. / Reutzel, R. / Mikulski, R. / McKenna, R. / Silverman, D.N.
CitationJournal: FREE RADIC.BIOL.MED. / Year: 2006
Title: Crystal structure of nitrated human manganese superoxide dismutase: mechanism of inactivation.
Authors: Quint, P. / Reutzel, R. / Mikulski, R. / McKenna, R. / Silverman, D.N.
History
DepositionJul 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superoxide dismutase [Mn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3723
Polymers22,2781
Non-polymers942
Water82946
1
A: Superoxide dismutase [Mn]
hetero molecules

A: Superoxide dismutase [Mn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7446
Polymers44,5562
Non-polymers1884
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+11/61
Unit cell
Length a, b, c (Å)81.270, 81.270, 242.181
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe assymmetric unit is a homodimer. The tetramer can be created by applying crystallographc symmetry to this dimer.

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Components

#1: Protein Superoxide dismutase [Mn]


Mass: 22278.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P04179, superoxide dismutase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 3 M Ammonium Sulfate, 100 mM Malate, 100 mM imidazole, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 14, 2005 / Details: Osmic blue
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 231776 / Num. obs: 60459 / % possible obs: 91.3 % / Observed criterion σ(F): 30 / Observed criterion σ(I): 30 / Redundancy: 3 % / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 30
Reflection shellResolution: 2.4→20 Å / Redundancy: 2 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 15 / Num. unique all: 1503 / Rsym value: 0.149 / % possible all: 80.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Wild-type human manganese superoxide dismutase with all tyrosines mutated to alanine

Resolution: 2.4→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 6046 -RANDOM
Rwork0.197 ---
all0.197 231776 --
obs0.197 60459 91.3 %-
Displacement parametersBiso mean: 33 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1557 0 2 46 1605
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.3
X-RAY DIFFRACTIONc_bond_d0.006

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