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- PDB-5t30: Human MnSOD-azide complex -

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Basic information

Entry
Database: PDB / ID: 5t30
TitleHuman MnSOD-azide complex
ComponentsSuperoxide dismutase [Mn], mitochondrial
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / Inhibitor / Azide / Complex / OXIDOREDUCTASE-OXIDOREDUCTASE inhibitor complex
Function / homology
Function and homology information


acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / negative regulation of membrane hyperpolarization / : / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / response to silicon dioxide / response to selenium ion / response to L-ascorbic acid / intracellular oxygen homeostasis / response to superoxide ...acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / negative regulation of membrane hyperpolarization / : / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / response to silicon dioxide / response to selenium ion / response to L-ascorbic acid / intracellular oxygen homeostasis / response to superoxide / response to manganese ion / hydrogen peroxide biosynthetic process / response to zinc ion / superoxide metabolic process / positive regulation of vascular associated smooth muscle cell apoptotic process / superoxide dismutase / Detoxification of Reactive Oxygen Species / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / superoxide dismutase activity / response to immobilization stress / response to isolation stress / negative regulation of vascular associated smooth muscle cell proliferation / mitochondrial nucleoid / response to electrical stimulus / response to cadmium ion / cellular response to ethanol / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Mitochondrial unfolded protein response (UPRmt) / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / removal of superoxide radicals / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / response to activity / response to hydrogen peroxide / Transcriptional activation of mitochondrial biogenesis / oxygen binding / regulation of blood pressure / manganese ion binding / negative regulation of neuron apoptotic process / response to lipopolysaccharide / cellular response to oxidative stress / response to hypoxia / protein homotetramerization / response to xenobiotic stimulus / positive regulation of cell migration / mitochondrial matrix / 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
AZIDE ION / : / : / PHOSPHATE ION / Superoxide dismutase [Mn], mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsAzadmanesh, J. / Trickel, S.R. / Kolar, C.H. / Lovelace, J.J. / Borgstahl, G.E.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Aeronautic Space Administration (NASA, United States)NNX15AM82A United States
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Substrate-analog binding and electrostatic surfaces of human manganese superoxide dismutase.
Authors: Azadmanesh, J. / Trickel, S.R. / Borgstahl, G.E.O.
History
DepositionAug 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 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 / database_2 / diffrn_radiation_wavelength / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1499
Polymers44,7292
Non-polymers4207
Water6,377354
1
A: Superoxide dismutase [Mn], mitochondrial
B: Superoxide dismutase [Mn], mitochondrial
hetero molecules

A: Superoxide dismutase [Mn], mitochondrial
B: Superoxide dismutase [Mn], mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,29718
Polymers89,4574
Non-polymers84014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area8420 Å2
ΔGint-45 kcal/mol
Surface area31660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.900, 77.900, 238.442
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 0 - 198 / Label seq-ID: 1 - 199

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Superoxide dismutase [Mn], mitochondrial


Mass: 22364.307 Da / Num. of mol.: 2 / Fragment: UNP residues 25-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD2 / Production host: Escherichia coli (E. coli) / References: UniProt: P04179, superoxide dismutase

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Non-polymers , 5 types, 361 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.8M potassium phosphate, pH 7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 2, 2016
RadiationMonochromator: OSMIC VARIMAX CONFOCAL MAX-FLUX OPTIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→67.5 Å / Num. obs: 40981 / % possible obs: 96 % / Redundancy: 5.6 % / Net I/σ(I): 12.7
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2 / % possible all: 84

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Coot0.8.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→67.46 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.914 / SU B: 2.918 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1964 4.9 %RANDOM
Rwork0.209 ---
obs0.21 38096 94.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.16 Å20 Å2
2---0.32 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.77→67.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 17 354 3533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193287
X-RAY DIFFRACTIONr_bond_other_d0.0020.023055
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.9334446
X-RAY DIFFRACTIONr_angle_other_deg0.91237025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4445398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15625.031159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.715531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.554158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213763
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02793
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1381.8471592
X-RAY DIFFRACTIONr_mcbond_other1.1341.8431591
X-RAY DIFFRACTIONr_mcangle_it1.8742.7551987
X-RAY DIFFRACTIONr_mcangle_other1.8742.7591988
X-RAY DIFFRACTIONr_scbond_it1.4632.0371695
X-RAY DIFFRACTIONr_scbond_other1.4632.0371696
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3512.9672459
X-RAY DIFFRACTIONr_long_range_B_refined3.64622.0923892
X-RAY DIFFRACTIONr_long_range_B_other3.48321.7463794
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 13236 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.77→1.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 111 -
Rwork0.277 2161 -
obs--74.39 %

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