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- PDB-3kky: Structure of Manganese Superoxide Dismutase from Deinococcus Radi... -

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Basic information

Entry
Database: PDB / ID: 3kky
TitleStructure of Manganese Superoxide Dismutase from Deinococcus Radiodurans in the orthorhombic space group P212121: A case study of mistaken identity
ComponentsSuperoxide dismutase [Mn]
KeywordsMETAL BINDING PROTEIN / Superoxide dismutase / deinococcus radiodurans / Manganese / Metal-binding / Oxidoreductase
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / metal ion binding / cytoplasm
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 / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Superoxide dismutase [Mn]
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGovindasamy, L. / Mikulski, R. / McKenna, M.A. / Silverman, D.N. / McKenna, R.
CitationJournal: To be Published
Title: Structure of Manganese Superoxide dismutase from Deinococcus Radiodurans in the orthorhombic space group P212121: A case study of mistaken identity
Authors: Govindasamy, L. / Mikulski, R. / McKenna, M.A. / Silverman, D.N. / McKenna, R.
History
DepositionNov 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 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

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Assembly

Deposited unit
A: Superoxide dismutase [Mn]
B: Superoxide dismutase [Mn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1184
Polymers47,0082
Non-polymers1102
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-11 kcal/mol
Surface area17610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.15, 80.24, 85.41
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Superoxide dismutase [Mn] / MnSOD


Mass: 23504.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: sodA, DR_1279 / Plasmid: pet31f1(-) / Production host: Escherichia coli (E. coli) / Strain (production host): QC774 / References: UniProt: Q9RUV2, superoxide dismutase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05M K2PO4, 16% PEG, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: osmic
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 34999 / % possible obs: 90 % / Redundancy: 24.8 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 4.1
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.385 / Num. unique all: 3527 / % possible all: 91.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ce4

2ce4


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.208 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1758 5 %RANDOM
Rwork0.166 ---
obs0.166 34999 90 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.223 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3228 0 2 162 3392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213359
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.9174577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3015416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30924.831178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.85715516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8481515
X-RAY DIFFRACTIONr_chiral_restr0.1270.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022671
X-RAY DIFFRACTIONr_nbd_refined0.1910.21334
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22319
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2122
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.9650.23
X-RAY DIFFRACTIONr_mcbond_it0.9941.52100
X-RAY DIFFRACTIONr_mcangle_it1.63623270
X-RAY DIFFRACTIONr_scbond_it2.46831470
X-RAY DIFFRACTIONr_scangle_it3.9024.51303
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 127 -
Rwork0.182 2434 -
obs--91.4 %

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