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- PDB-7kkw: Neutron structure of Reduced Human MnSOD -

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Basic information

Entry
Database: PDB / ID: 7kkw
TitleNeutron structure of Reduced Human MnSOD
ComponentsSuperoxide dismutase [Mn], mitochondrial
KeywordsOXIDOREDUCTASE / Antioxidant / SOD / Superoxide
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 / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / respiratory electron transport chain / glutathione metabolic process / release of cytochrome c from mitochondria / post-embryonic development / regulation of mitochondrial membrane potential / liver development / response to activity / locomotory behavior / response to gamma radiation / response to hydrogen peroxide / Transcriptional activation of mitochondrial biogenesis / 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 / heart development / manganese ion binding / 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
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
Similarity search - Domain/homology
: / DEUTERATED WATER / : / Superoxide dismutase [Mn], mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodNEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAzadmanesh, J. / Lutz, W.E. / Coates, L. / Weiss, K.L. / Borgstahl, G.E.O.
Funding support United States, 2items
OrganizationGrant numberCountry
National Aeronautics and Space Administration (NASA, United States)44-0307-1021-201 United States
Department of Energy (DOE, United States) United States
CitationJournal: Nat Commun / Year: 2021
Title: Direct detection of coupled proton and electron transfers in human manganese superoxide dismutase.
Authors: Azadmanesh, J. / Lutz, W.E. / Coates, L. / Weiss, K.L. / Borgstahl, G.E.O.
History
DepositionOct 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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
Revision 2.0Apr 10, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_symm_contact / refine_ls_restr_ncs / software / struct_asym / struct_conn / struct_ncs_dom_lim / struct_ncs_oper
Item: _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_comp_id ..._atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _entity_src_gen.gene_src_common_name / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_comp_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_special_symmetry.auth_comp_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_struct_special_symmetry.label_comp_id / _refine_ls_restr_ncs.pdbx_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][2] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _struct_ncs_oper.matrix[3][3] / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[2] / _struct_ncs_oper.vector[3]
Description: Model completeness
Details: For some reason, the atoms below were removed during the original deposition process. I just re-uploaded the same mmcif file and the atoms are now there. These D atoms observed from neutron ...Details: For some reason, the atoms below were removed during the original deposition process. I just re-uploaded the same mmcif file and the atoms are now there. These D atoms observed from neutron crystallography are intended to represent protons participating in unusual hydrogen bonds, such as a low-barrier hydrogen bond. From the .cif deposition file: HETATM 6555 D D1 . HOH E 3 . ? 14.92010 40.17563 92.77950 1.000 25.96690 ? 166 HOH S D1 166 HOH S D1 1 HETATM 6526 D D1 . HOH E 3 . ? 8.43799 43.24591 94.59324 1.000 20.84612 ? 140 HOH S D1 140 HOH S D1 1 HETATM 6556 D D2 . HOH E 3 . ? 46.12570 26.33746 94.54097 1.000 21.81906 ? 201 HOH S D2 201 HOH S D2 1 HETATM 6525 D D1 . HOH E 3 . ? 51.61148 18.67575 94.22714 1.000 27.96372 ? 141 HOH S D1 141 HOH S D1 1 PDB Format: HETATM 6555 D1 HOH S 166 14.920 40.176 92.780 1.00 25.97 D HETATM 6526 D1 HOH S 140 8.438 43.246 94.593 1.00 20.85 D HETATM 6556 D2 HOH S 201 46.126 26.337 94.541 1.00 21.82 D HETATM 6525 D1 HOH S 141 51.611 18.676 94.227 1.00 27.96 D
Provider: author / Type: Coordinate replacement

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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)44,8478
Polymers44,7292
Non-polymers1186
Water2,144119
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)89,69316
Polymers89,4574
Non-polymers23612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)81.330, 81.330, 242.880
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-345-

DOD

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 0 - 198 / Label seq-ID: 1 - 199

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.982170008569, 0.0257767817966, -0.186219310993), (0.0321281002602, -0.952967905783, -0.301363494339), (-0.185229207849, -0.301973058512, 0.93514833716)Vector: 75. ...NCS oper: (Code: given
Matrix: (-0.982170008569, 0.0257767817966, -0.186219310993), (0.0321281002602, -0.952967905783, -0.301363494339), (-0.185229207849, -0.301973058512, 0.93514833716)
Vector: 75.8636305835, 88.2507120574, 21.2663416867)

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Components

#1: Protein Superoxide dismutase [Mn], mitochondrial


Mass: 22364.307 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-D8U / deuterium(1+)


Mass: 2.014 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: D
#4: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: D2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 1.93 M Potassium Phosphate

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Data collection

DiffractionMean temperature: 296 K / Serial crystal experiment: N
Diffraction sourceSource: SPALLATION SOURCE / Site: ORNL Spallation Neutron Source / Beamline: MANDI / Wavelength: 2-4
DetectorType: ORNL ANGER CAMERA / Detector: DIFFRACTOMETER / Date: Oct 30, 2018
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
121
241
ReflectionResolution: 2.3→14.65 Å / Num. obs: 21719 / % possible obs: 98.94 % / Redundancy: 7.2 % / Biso Wilson estimate: 17.92 Å2 / CC1/2: 0.943 / Rmerge(I) obs: 0.277 / Rpim(I) all: 0.102 / Net I/σ(I): 6.2
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2116 / CC1/2: 0.319 / Rpim(I) all: 0.124 / % possible all: 99.16

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Processing

Software
NameClassification
Mantiddata reduction
LaueViewdata scaling
PHENIXrefinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VF9

5vf9


Resolution: 2.3→14.65 Å / SU ML: 0.4028 / Cross valid method: FREE R-VALUE / σ(F): 2.3 / Phase error: 25.8142
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3021 1086 5 %
Rwork0.2493 20628 -
obs0.252 21714 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.01 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.00393254
NEUTRON DIFFRACTIONf_angle_d0.6554418
NEUTRON DIFFRACTIONf_chiral_restr0.0393454
NEUTRON DIFFRACTIONf_plane_restr0.0043576
NEUTRON DIFFRACTIONf_dihedral_angle_d17.64011172
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.608011922946 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40.37051330.31492522NEUTRON DIFFRACTION99.14
2.4-2.530.38981310.31522509NEUTRON DIFFRACTION98.77
2.53-2.690.3221330.30112510NEUTRON DIFFRACTION99.06
2.69-2.890.36741340.29012549NEUTRON DIFFRACTION99.04
2.89-3.180.3281340.25932557NEUTRON DIFFRACTION99.34
3.18-3.640.26311360.23462591NEUTRON DIFFRACTION99.42
3.64-4.560.24421410.1962648NEUTRON DIFFRACTION99.57
4.56-14.650.26141440.20522742NEUTRON DIFFRACTION97.3
Refinement TLS params.Method: refined / Origin x: 30.0402186197 Å / Origin y: 31.4675959518 Å / Origin z: 92.813791277 Å
111213212223313233
T0.209781046786 Å2-0.0232314464754 Å2-0.0341650857771 Å2-0.190489484416 Å20.000662399520967 Å2--0.179153585179 Å2
L1.16451051942 °2-0.240886330346 °20.0229705693592 °2-0.135156868284 °2-0.0139323610934 °2--0.112689915831 °2
S-0.0346440429909 Å °0.0200294941716 Å °-0.0240586658434 Å °0.0297771256477 Å °0.0294626774901 Å °-0.0261266064789 Å °-0.0139744818222 Å °0.00748552262137 Å °0.0169347006929 Å °
Refinement TLS groupSelection details: all

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