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- PDB-4e4e: Crystal Structure of the Y34F mutant of Saccharomyces cerevisiae ... -

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Basic information

Entry
Database: PDB / ID: 4e4e
TitleCrystal Structure of the Y34F mutant of Saccharomyces cerevisiae Manganese Superoxide Dismutase
ComponentsSuperoxide dismutase [Mn], mitochondrial
KeywordsOXIDOREDUCTASE / Mn Superoxide Dismutase
Function / homology
Function and homology information


Transcriptional activation of mitochondrial biogenesis / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsSheng, Y. / Cascio, D. / Valentine, J.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Six-coordinate manganese(3+) in catalysis by yeast manganese superoxide dismutase.
Authors: Sheng, Y. / Butler Gralla, E. / Schumacher, M. / Cascio, D. / Cabelli, D.E. / Selverstone Valentine, J.
History
DepositionMar 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Sep 13, 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_ref_seq_dif / 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_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_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

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)94,3188
Polymers94,0994
Non-polymers2204
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-84 kcal/mol
Surface area32570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.139, 63.022, 63.943
Angle α, β, γ (deg.)112.190, 106.780, 103.880
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Superoxide dismutase [Mn], mitochondrial


Mass: 23524.674 Da / Num. of mol.: 4 / Mutation: Y34F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: EG110 / Gene: SOD2, YHR008C / Plasmid: YEp352 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M 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: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9641 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2011
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9641 Å / Relative weight: 1
ReflectionResolution: 1.88→100 Å / Num. obs: 59948 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.122 / Χ2: 1.394 / Net I/σ(I): 5.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.88-1.972.70.54759601.094196.3
1.97-2.052.80.42360051.077196.4
2.05-2.142.80.32360310.978197
2.14-2.252.90.25659550.903197
2.25-2.392.90.20360270.921197.1
2.39-2.582.90.16560760.95197.6
2.58-2.842.90.13160541.136197.6
2.84-3.252.80.10860701.608197.8
3.25-4.092.70.08959612.38196.3
4.09-1002.80.08358093.098193.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å52.66 Å
Translation2.5 Å52.66 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LSU

3lsu


Resolution: 1.88→32.183 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8227 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 25.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 3041 5.08 %RANDOM
Rwork0.1898 ---
obs0.1919 59832 94.55 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.64 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso max: 71.69 Å2 / Biso mean: 28.4332 Å2 / Biso min: 13.89 Å2
Baniso -1Baniso -2Baniso -3
1-1.2609 Å20.8123 Å21.8178 Å2
2--5.7709 Å2-9.6207 Å2
3----7.0319 Å2
Refinement stepCycle: LAST / Resolution: 1.88→32.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6613 0 4 231 6848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096839
X-RAY DIFFRACTIONf_angle_d1.1499321
X-RAY DIFFRACTIONf_chiral_restr0.08967
X-RAY DIFFRACTIONf_plane_restr0.0051192
X-RAY DIFFRACTIONf_dihedral_angle_d15.7212455
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 (%)
1.88-1.90950.3055790.29431489156854
1.9095-1.94090.32961350.24672557269296
1.9409-1.97430.30281750.24392617279296
1.9743-2.01020.30031360.21942640277697
2.0102-2.04890.23511450.21132585273096
2.0489-2.09070.2631440.20292660280497
2.0907-2.13610.26781370.20212649278697
2.1361-2.18580.23951490.18972630277997
2.1858-2.24050.24541530.20432626277997
2.2405-2.3010.26021260.18492647277397
2.301-2.36870.21321350.18882671280697
2.3687-2.44510.27521520.18422675282798
2.4451-2.53250.26241300.19842638276897
2.5325-2.63390.25031430.20372698284198
2.6339-2.75370.2921290.20292649277897
2.7537-2.89880.22111420.2152655279798
2.8988-3.08020.241420.21032699284198
3.0802-3.31780.23841480.19292641278998
3.3178-3.65130.20381510.17692606275797
3.6513-4.17870.2041390.16012629276896
4.1787-5.2610.18721350.162551268693
5.261-32.18730.18441160.17462579269594

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