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- PDB-1my6: The 1.6 A Structure of Fe-Superoxide Dismutase from the thermophi... -

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Basic information

Entry
Database: PDB / ID: 1my6
TitleThe 1.6 A Structure of Fe-Superoxide Dismutase from the thermophilic cyanobacterium Thermosynechococcus elongatus : Correlation of EPR and Structural Characteristics
ComponentsIron (III) Superoxide Dismutase
KeywordsOXIDOREDUCTASE / Iron Speroxide Dismutase / thermophile / reactive oxygen species / cyanobacteria / thermosynechococcus / Thermosynechococcus elongatus / Superoxide Dismutase / SOD / FeSOD / Iron(III) Superoxide Dismutase
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
: / Superoxide dismutase
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYoshida, S.M. / Cascio, D. / Sawaya, M.R. / Yeates, T.O. / Kerfeld, C.A.
CitationJournal: J.BIOL.INORG.CHEM. / Year: 2003
Title: The 1.6 A resolution structure of Fe-superoxide dismutase from the thermophilic cyanobacterium Thermosynechococcus elongatus.
Authors: Kerfeld, C.A. / Yoshida, S. / Tran, K.T. / Yeates, T.O. / Cascio, D. / Bottin, H. / Berthomieu, C. / Sugiura, M. / Boussac, A.
History
DepositionOct 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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_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_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_conn.ptnr2_label_seq_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: Iron (III) Superoxide Dismutase
B: Iron (III) Superoxide Dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3254
Polymers44,2132
Non-polymers1122
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-12 kcal/mol
Surface area16370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.749, 63.644, 74.709
Angle α, β, γ (deg.)90.00, 110.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Iron (III) Superoxide Dismutase


Mass: 22106.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q8DIR2, superoxide dismutase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: VAPOR DIFFUSION, HANGING DROP, 293.15K, 0.1M Sodium Cacodylate pH 6.7, 0.2M Magnesium Acetate Tetrahydrate, 20% PEG 6K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111.7 mg/mlprotein1drop
210 mMTris1droppH7.5
30.1 Msodium cacodylate1reservoirpH6.7
40.2 Mmagnesium acetate tetrahydrate1reservoir
520 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 2, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.6→70 Å / Num. obs: 53851 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 16.18 % / Biso Wilson estimate: 15.3 Å2 / Rsym value: 0.088 / Net I/σ(I): 6.35
Reflection shellResolution: 1.6→1.642 Å / Redundancy: 14.28 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 6.35 / Num. unique all: 5643 / Rsym value: 0.32 / % possible all: 93.4
Reflection
*PLUS
% possible obs: 99.57 % / Num. measured all: 274614 / Rmerge(I) obs: 0.088
Reflection shell
*PLUS
Lowest resolution: 1.66 Å / % possible obs: 94.5 % / Rmerge(I) obs: 0.322

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FeSOD from E.coli, PDB entry 1isc

1isc


Resolution: 1.6→70 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.923 / SU B: 1.748 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Refined with anisotropic temperature factors. NCS restraints were not applied on the 2 molecules in the asymmetric unit.
RfactorNum. reflection% reflectionSelection details
Rfree0.23208 2896 5.1 %RANDOM
Rwork0.19377 ---
obs0.19577 53851 94.46 %-
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: 15.669 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å20.82 Å2
2---1.54 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.6→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 2 565 3695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213224
X-RAY DIFFRACTIONr_bond_other_d0.0020.022744
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9144396
X-RAY DIFFRACTIONr_angle_other_deg0.90336392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.885394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023686
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02686
X-RAY DIFFRACTIONr_nbd_refined0.2310.2739
X-RAY DIFFRACTIONr_nbd_other0.2470.23169
X-RAY DIFFRACTIONr_nbtor_other0.0870.21715
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2387
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.3121.51966
X-RAY DIFFRACTIONr_mcangle_it1.9123138
X-RAY DIFFRACTIONr_scbond_it2.61631258
X-RAY DIFFRACTIONr_scangle_it3.6934.51258
X-RAY DIFFRACTIONr_rigid_bond_restr1.52223224
X-RAY DIFFRACTIONr_sphericity_free3.6712567
X-RAY DIFFRACTIONr_sphericity_bonded2.12423130
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.25 215
Rwork0.159 4063
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.226 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2

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