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- PDB-2goj: The crystal structure of the enzyme Fe-superoxide dismutase from ... -

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Basic information

Entry
Database: PDB / ID: 2goj
TitleThe crystal structure of the enzyme Fe-superoxide dismutase from Plasmodium falciparum
ComponentsFe-superoxide dismutase
KeywordsOXIDOREDUCTASE / BETA+ALPHA STRUCTURE
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 [Fe]
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNavarro, M.V.A.S. / Garratt, R.C.
CitationJournal: Proteins / Year: 2009
Title: Systematic structural studies of iron superoxide dismutases from human parasites and a statistical coupling analysis of metal binding specificity
Authors: Bachega, J.F. / Navarro, M.V. / Bleicher, L. / Bortoleto-Bugs, R.K. / Dive, D. / Hoffmann, P. / Viscogliosi, E. / Garratt, R.C.
History
DepositionApr 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Fe-superoxide dismutase
B: Fe-superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3734
Polymers45,2612
Non-polymers1122
Water5,495305
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.402, 78.417, 88.369
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe assymetric unit contains a dimer, which represents the molecular assembly

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Components

#1: Protein Fe-superoxide dismutase


Mass: 22630.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: HB3 / Gene: SOD / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12
References: GenBank: 861077, UniProt: Q27740*PLUS, superoxide dismutase
#2: Chemical ChemComp-FE2 / FE (II) 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.: 305 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25.5% PEG 4000 (w/v), 0.17 M Sodium Acetate, 0.085 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 10, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→31.62 Å / Num. obs: 25131 / % possible obs: 95.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rsym value: 0.098 / Net I/σ(I): 7.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2 / Rsym value: 0.37 / % possible all: 73.3

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Processing

SoftwareName: REFMAC / Version: 5.1.24 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ISA

1isa


Resolution: 2→31.62 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.711 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.191 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19389 1266 5 %RANDOM
Rwork0.15576 ---
obs0.15769 24057 94.97 %-
all-24057 --
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: 14.498 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→31.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 2 305 3482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213315
X-RAY DIFFRACTIONr_bond_other_d0.0020.022768
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.8994511
X-RAY DIFFRACTIONr_angle_other_deg0.79636507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5765397
X-RAY DIFFRACTIONr_chiral_restr0.0720.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023733
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02679
X-RAY DIFFRACTIONr_nbd_refined0.1950.2738
X-RAY DIFFRACTIONr_nbd_other0.2320.23172
X-RAY DIFFRACTIONr_nbtor_other0.0840.21626
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2210
X-RAY DIFFRACTIONr_metal_ion_refined0.040.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2730.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.215
X-RAY DIFFRACTIONr_mcbond_it0.551.51953
X-RAY DIFFRACTIONr_mcangle_it1.05323142
X-RAY DIFFRACTIONr_scbond_it1.55831362
X-RAY DIFFRACTIONr_scangle_it2.5254.51365
LS refinement shellResolution: 2→2.108 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.242 136
Rwork0.201 2582

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