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- PDB-3lsu: Crystal Structure of SOD2 from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 3lsu
TitleCrystal Structure of SOD2 from Saccharomyces cerevisiae
ComponentsSuperoxide dismutase [Mn], mitochondrial
KeywordsOXIDOREDUCTASE / Mn Superoxide Dismutase / reductive methylation / Manganese / Metal-binding / Mitochondrion / Phosphoprotein / Transit peptide
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 (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.896 Å
AuthorsSheng, Y. / Cascio, D. / Valentine, J.S.
CitationJournal: To be Published
Title: Crystal Structure of SOD2 from Saccharomyces cerevisiae
Authors: Sheng, Y. / Cascio, D. / Valentine, J.S.
History
DepositionFeb 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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

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)94,77413
Polymers94,1634
Non-polymers6119
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12380 Å2
ΔGint-86 kcal/mol
Surface area32560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.657, 64.933, 66.550
Angle α, β, γ (deg.)109.360, 106.350, 109.680
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Superoxide dismutase [Mn], mitochondrial


Mass: 23540.674 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SOD2, YHR008C / Plasmid: YEp352-SOD2 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): EG103 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M sodium malonate, 20% PEG 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+ DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 23, 2009
RadiationMonochromator: CONFOCAL MIRRORS Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→80 Å / Num. obs: 59997 / % possible obs: 89.5 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.083 / Χ2: 1.194 / Net I/σ(I): 14.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3538 / Rsym value: 0.314 / Χ2: 0.947 / % possible all: 53.1

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Phasing

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

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.2phasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QNM

1qnm


Resolution: 1.896→32.376 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.876 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.195 3032 5.06 %RANDOM
Rwork0.162 ---
obs0.163 59978 89.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.979 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso max: 72.48 Å2 / Biso mean: 24.841 Å2 / Biso min: 13.32 Å2
Baniso -1Baniso -2Baniso -3
1-2.047 Å2-0.694 Å21.871 Å2
2--2.233 Å2-2.437 Å2
3----4.28 Å2
Refine analyzeLuzzati sigma a obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.896→32.376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6656 0 29 421 7106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076858
X-RAY DIFFRACTIONf_angle_d1.0459331
X-RAY DIFFRACTIONf_chiral_restr0.073901
X-RAY DIFFRACTIONf_plane_restr0.0411251
X-RAY DIFFRACTIONf_dihedral_angle_d24.7022619
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.896-1.9260.192630.1651219128243
1.926-1.9580.209760.1731656173256
1.958-1.9910.246950.1661915201066
1.991-2.0280.1931500.1552439258985
2.028-2.0670.2231350.1592750288593
2.067-2.1090.1951390.1562675281493
2.109-2.1550.2141480.1552683283193
2.155-2.2050.2231520.1562724287694
2.205-2.260.2231520.162700285294
2.26-2.3210.1851480.1552735288394
2.321-2.3890.1821470.1522764291194
2.389-2.4660.2011560.1622725288195
2.466-2.5550.2121410.1612788292995
2.555-2.6570.2171790.1692709288895
2.657-2.7770.2361440.1712809295396
2.777-2.9240.2231350.1822788292396
2.924-3.1070.2231450.1812802294796
3.107-3.3470.181500.1692802295297
3.347-3.6830.1891460.1542815296197
3.683-4.2150.161420.1382799294196
4.215-5.3060.1481460.1512799294596
5.306-32.3810.1771430.1622850299398

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