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- PDB-3k9s: Crystal structure of the peroxide-bound manganese superoxide dism... -

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Basic information

Entry
Database: PDB / ID: 3k9s
TitleCrystal structure of the peroxide-bound manganese superoxide dismutase.
ComponentsSuperoxide dismutase [Mn]
KeywordsOXIDOREDUCTASE / Manganese superoxide dismutase / peroxide-bound / Manganese / Metal-binding
Function / homology
Function and homology information


cellular response to selenium ion / response to acidic pH / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / antioxidant activity / removal of superoxide radicals / manganese ion binding / response to heat / response to oxidative stress ...cellular response to selenium ion / response to acidic pH / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / antioxidant activity / removal of superoxide radicals / manganese ion binding / response to heat / response to oxidative stress / protein homodimerization activity / DNA binding / metal ion binding / cytoplasm / cytosol
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
: / HYDROGEN PEROXIDE / Superoxide dismutase [Mn]
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsPorta, J.C. / Vahedi-Faridi, A. / Borgstahl, G.E.O.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural Analysis of Peroxide-Soaked MnSOD Crystals Reveals Side-On Binding of Peroxide to Active-Site Manganese.
Authors: Porta, J. / Vahedi-Faridi, A. / Borgstahl, G.E.
History
DepositionOct 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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_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.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.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]
B: Superoxide dismutase [Mn]
C: Superoxide dismutase [Mn]
D: Superoxide dismutase [Mn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,30911
Polymers91,9884
Non-polymers3227
Water8,611478
1
A: Superoxide dismutase [Mn]
B: Superoxide dismutase [Mn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1385
Polymers45,9942
Non-polymers1443
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-13 kcal/mol
Surface area17580 Å2
MethodPISA
2
C: Superoxide dismutase [Mn]
D: Superoxide dismutase [Mn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1726
Polymers45,9942
Non-polymers1784
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-12 kcal/mol
Surface area17410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.849, 107.418, 180.044
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Superoxide dismutase [Mn] / MnSOD


Mass: 22996.877 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b3908, JW3879, sodA / Plasmid: pTTQA10 / Production host: Escherichia coli (E. coli) / Strain (production host): OX326A.1 / References: UniProt: P00448, 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-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2.65 Å3/Da / Density % sol: 53.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 50 mM Bicine pH 8.5, 25% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 8, 2000 / Details: Mirrors
RadiationMonochromator: Vertical focusing mirror single crystal (Si111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.55→28.3 Å / Num. all: 154389 / Num. obs: 139669 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 13.3 Å2 / Rsym value: 0.0822 / Net I/σ(I): 10.4
Reflection shellResolution: 1.55→1.61 Å / % possible all: 82

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1D5N

1d5n


Resolution: 1.55→28.3 Å / Cor.coef. Fo:Fc: 0.862 / Cor.coef. Fo:Fc free: 0.83 / SU B: 4.316 / SU ML: 0.072 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.133 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26998 6254 5 %RANDOM
Rwork0.22711 ---
obs0.22926 118082 88.23 %-
all-154389 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.295 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.83 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.55→28.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6512 0 10 478 7000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226725
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.9319091
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8745818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30224.568324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.158151085
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7991524
X-RAY DIFFRACTIONr_chiral_restr0.0890.2949
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215200
X-RAY DIFFRACTIONr_mcbond_it0.7831.54089
X-RAY DIFFRACTIONr_mcangle_it1.1126510
X-RAY DIFFRACTIONr_scbond_it1.80932636
X-RAY DIFFRACTIONr_scangle_it2.4084.52580
X-RAY DIFFRACTIONr_rigid_bond_restr1.10636725
X-RAY DIFFRACTIONr_sphericity_free4.7333481
X-RAY DIFFRACTIONr_sphericity_bonded2.26436523
LS refinement shellResolution: 1.551→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 373 -
Rwork0.227 6479 -
obs--66.27 %

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