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- PDB-1unf: The crystal structure of the eukaryotic FeSOD from Vigna unguicul... -

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Basic information

Entry
Database: PDB / ID: 1unf
TitleThe crystal structure of the eukaryotic FeSOD from Vigna unguiculata suggests a new enzymatic mechanism
ComponentsIRON SUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE / EUKARYOTIC / SUPEROXIDE DISMUTASE / METALLOPROTEIN
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding
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 / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily
Similarity search - Domain/homology
: / Superoxide dismutase
Similarity search - Component
Biological speciesVIGNA UNGUICULATA (cowpea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsMunoz, I.G. / Moran, J.F. / Becana, M. / Montoya, G.
CitationJournal: Protein Sci. / Year: 2005
Title: The Crystal Structure of an Eukaryotic Iron Superoxide Dismutase Suggests Intersubunit Cooperation During Catalysis
Authors: Munoz, I.G. / Moran, J.F. / Becana, M. / Montoya, G.
History
DepositionSep 10, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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
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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: IRON SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7952
Polymers26,7391
Non-polymers561
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)81.985, 48.163, 63.671
Angle α, β, γ (deg.)90.00, 119.76, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-2135-

HOH

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Components

#1: Protein IRON SUPEROXIDE DISMUTASE / / SUPEROXIDE DISMUTASE [MN/FE]


Mass: 26739.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) VIGNA UNGUICULATA (cowpea) / Cellular location: CYTOSOL / Strain: VUFESOD / Tissue: LEGUME ROOT NODULES / References: UniProt: Q9M7R2, superoxide dismutase
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.23 Å3/Da / Density % sol: 44.46 %
Crystal growpH: 5
Details: 200 MM AMMONIUM SULFATE, 100 MM SODIUM ACETATE PH 5.0, 25%(W/V) POLYETHYLENE GLYCOL 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.033
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 20443 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 0.9 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DT0

1dt0


Resolution: 1.97→28.77 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.356 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R Free: 0.139
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.192 772 5 %RANDOM
Rwork0.148 ---
obs0.15 14661 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.97→28.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1724 0 1 184 1909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221775
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.9432409
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7645211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37524.82485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26215289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.073155
X-RAY DIFFRACTIONr_chiral_restr0.190.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021371
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.3940
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3230.51227
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.5242
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0760.51
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.331
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3620.529
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.28121091
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.3831706
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4342807
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4413703
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.02 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 57 -
Rwork0.146 1024 -
obs--96.17 %

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