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- PDB-4f6e: Crystal Structure of the K182R, A183P mutant manganese superoxide... -

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Entry
Database: PDB / ID: 4f6e
TitleCrystal Structure of the K182R, A183P mutant manganese superoxide dismutase from Sacchromyces cerevisiae
ComponentsSuperoxide dismutase [Mn], mitochondrial
KeywordsOXIDOREDUCTASE / Mn Superoxide Dismutase / dimer interface
Function / homology
Function and homology information


Detoxification of Reactive Oxygen Species / superoxide dismutase / superoxide dismutase activity / reactive oxygen species metabolic process / manganese ion binding / mitochondrial matrix / mitochondrion
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 speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsSheng, Y. / Cascio, D. / Valentine, J.S.
CitationJournal: to be published
Title: Crystal Structure of the K182R, A183P mutant manganese superoxide dismutase from Sacchromyces cerevisiae
Authors: Sheng, Y. / Cascio, D. / Valentine, J.S.
History
DepositionMay 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 2.0Feb 22, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.label_asym_id
Revision 2.1Sep 20, 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)94,70510
Polymers94,2714
Non-polymers4346
Water9,998555
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11570 Å2
ΔGint-83 kcal/mol
Surface area33010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.540, 66.250, 66.620
Angle α, β, γ (deg.)112.580, 103.630, 110.270
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Superoxide dismutase [Mn], mitochondrial


Mass: 23567.680 Da / Num. of mol.: 4 / Mutation: K182R, A183P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: SOD2, YHR008C / Plasmid: YEp352-SOD2 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): EG110 / References: UniProt: P00447, superoxide dismutase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.4 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M tri-ammonium citrate, 20% (w/v) polyethylene glycol 3350, pH 7.0, vapor diffusion, hanging drop, temperature 277K

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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 HTC / Detector: IMAGE PLATE / Date: Oct 7, 2011
RadiationMonochromator: CONFOCAL MIRRORS Varimax HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→37.653 Å / Num. obs: 105023 / % possible obs: 90.2 % / Observed criterion σ(I): -3 / Redundancy: 3.82 % / Biso Wilson estimate: 22.496 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 22.69
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.6-1.640.176.79209076075170.8
1.64-1.690.1528.33282047285187.4
1.69-1.730.1359.31278777182188
1.73-1.790.10811.3274467075188.7
1.79-1.850.09312.75266296868189.2
1.85-1.910.07615.21258156663190.3
1.91-1.980.06317.78251586505190.5
1.98-2.060.05420.71243376292191
2.06-2.160.04723.64235146096191.9
2.16-2.260.04126.33224695833192.5
2.26-2.380.0427.68215725619193.1
2.38-2.530.03729.82204455331193.3
2.53-2.70.03432.04191695011194.2
2.7-2.920.03234.48179414726194.9
2.92-3.20.0336.96164914366195.3
3.2-3.580.02740.36149043977195.7
3.58-4.130.02443.03133393537196.4
4.13-5.060.02244.33112982991196.7
5.06-7.150.02542.6686652313197.6
7.15-37.650.02245.2847281278196.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å37.65 Å
Translation2.5 Å37.65 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LSU

3lsu


Resolution: 1.6→37.653 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8871 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 18.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 5252 5 %RANDOM
Rwork0.1643 ---
obs0.1658 105020 90.55 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.61 Å2 / ksol: 0.402 e/Å3
Displacement parametersBiso max: 69.11 Å2 / Biso mean: 17.1588 Å2 / Biso min: 5.64 Å2
Baniso -1Baniso -2Baniso -3
1-2.6758 Å2-1.7443 Å2-0.3807 Å2
2---1.342 Å20.3577 Å2
3----1.3338 Å2
Refinement stepCycle: LAST / Resolution: 1.6→37.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6642 0 29 555 7226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066860
X-RAY DIFFRACTIONf_angle_d1.0379348
X-RAY DIFFRACTIONf_chiral_restr0.078967
X-RAY DIFFRACTIONf_plane_restr0.0051197
X-RAY DIFFRACTIONf_dihedral_angle_d12.9862468
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5996-1.61770.23291110.19162094220557
1.6177-1.63680.22511570.18082984314181
1.6368-1.65670.21871660.17073167333387
1.6567-1.67770.22251720.17483262343488
1.6777-1.69980.23211700.16583227339788
1.6998-1.72310.17351700.16413224339488
1.7231-1.74770.20181720.16513276344888
1.7477-1.77380.20221710.16023248341989
1.7738-1.80150.19941730.15453294346789
1.8015-1.8310.18011730.16133286345990
1.831-1.86260.21231740.16293310348490
1.8626-1.89650.21521750.15513319349490
1.8965-1.93290.19691760.15633338351491
1.9329-1.97240.22411740.15593301347591
1.9724-2.01530.18841760.15493343351991
2.0153-2.06210.19181780.16373382356092
2.0621-2.11370.21391780.16353388356692
2.1137-2.17080.20351770.15963374355193
2.1708-2.23470.17231800.15973417359793
2.2347-2.30680.18371800.15833419359993
2.3068-2.38930.20271810.16623429361094
2.3893-2.48490.21541820.17283460364294
2.4849-2.5980.20051820.17163465364794
2.598-2.73490.20221840.17593492367694
2.7349-2.90620.22871830.1823478366195
2.9062-3.13050.20881850.18433509369496
3.1305-3.44530.17951860.17113540372696
3.4453-3.94340.17571870.15663557374497
3.9434-4.96650.16391880.14213564375297
4.9665-37.66330.19151910.16493621381298
Refinement TLS params.Method: refined / Origin x: -0.6978 Å / Origin y: -12.3594 Å / Origin z: -21.9457 Å
111213212223313233
T0.0135 Å20.0149 Å20.0235 Å2-0.0376 Å20.0091 Å2--0.0425 Å2
L0.313 °20.2306 °20.3548 °2-0.4126 °20.2606 °2--0.671 °2
S0.0204 Å °-0.0406 Å °-0.0269 Å °-0.0101 Å °-0.0165 Å °-0.0023 Å °-0.0116 Å °-0.0095 Å °0.0015 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 207
2X-RAY DIFFRACTION1allB1 - 205
3X-RAY DIFFRACTION1allC1 - 207
4X-RAY DIFFRACTION1allD1 - 301
5X-RAY DIFFRACTION1allA - D1 - 302
6X-RAY DIFFRACTION1allB1 - 555
7X-RAY DIFFRACTION1allD1 - 303
8X-RAY DIFFRACTION1allC1 - 302

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