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

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Basic information

Entry
Database: PDB / ID: 2gpc
TitleThe crystal structure of the enzyme Fe-superoxide dismutase from Trypanosoma cruzi
Componentsiron superoxide dismutase
KeywordsOXIDOREDUCTASE / ALPHA+BETA STRUCTURE
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 / 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 speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: iron superoxide dismutase
B: iron superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8955
Polymers43,7592
Non-polymers1363
Water8,251458
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.626, 38.985, 91.073
Angle α, β, γ (deg.)90.00, 105.85, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-723-

HOH

DetailsThe asymmetric unit contains a dimer, which represents the biological assembly

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Components

#1: Protein iron superoxide dismutase


Mass: 21879.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli (E. coli) / References: GenBank: 71650673, UniProt: Q4DI29*PLUS
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 24% PEG4000, 0.2 M MgCl2, 0.1 M TRIS-HCl, pH 8.0, 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: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 25, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→29.5 Å / Num. obs: 27127 / % possible obs: 94.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rsym value: 0.063 / Net I/σ(I): 10.6
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.276 / % possible all: 69.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ISA

1isa


Resolution: 1.9→29.49 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.122 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.164 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1981 1414 5 %RANDOM
Rwork0.15449 ---
obs0.15666 26598 94.56 %-
all-28012 --
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: 14.471 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 3 458 3568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213204
X-RAY DIFFRACTIONr_bond_other_d0.0020.022709
X-RAY DIFFRACTIONr_angle_refined_deg1.1181.9124366
X-RAY DIFFRACTIONr_angle_other_deg0.77936345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6945388
X-RAY DIFFRACTIONr_chiral_restr0.0690.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023601
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02663
X-RAY DIFFRACTIONr_nbd_refined0.1990.2683
X-RAY DIFFRACTIONr_nbd_other0.2280.23066
X-RAY DIFFRACTIONr_nbtor_other0.0810.21630
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2335
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1020.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2010.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.236
X-RAY DIFFRACTIONr_mcbond_it0.461.51932
X-RAY DIFFRACTIONr_mcangle_it0.87723103
X-RAY DIFFRACTIONr_scbond_it1.36631272
X-RAY DIFFRACTIONr_scangle_it2.234.51262
LS refinement shellResolution: 1.9→2.002 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.243 150
Rwork0.187 2821

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