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- PDB-2c0d: Structure of the mitochondrial 2-cys peroxiredoxin from Plasmodiu... -

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Basic information

Entry
Database: PDB / ID: 2c0d
TitleStructure of the mitochondrial 2-cys peroxiredoxin from Plasmodium falciparum
ComponentsTHIOREDOXIN PEROXIDASE 2
KeywordsOXIDOREDUCTASE / PEROXIREDOXIN / 2-CYS / PEROXIDASE / THIOREDOXIN DEPENDANT / MITOCHONDRIAL / ANTIOXIDANT / REDOX-ACTIVE CENTER
Function / homology
Function and homology information


peroxiredoxin / thioredoxin peroxidase activity / cellular response to stress / cell redox homeostasis / hydrogen peroxide catabolic process / response to oxidative stress / mitochondrion / cytosol
Similarity search - Function
Peroxiredoxin, AhpC-type / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Peroxiredoxin, AhpC-type / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin peroxidase 2 / Thioredoxin peroxidase 2
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsBoucher, I.W. / Brannigan, J.A. / Wilkinson, A.J. / Brzozowski, A.M. / Muller, S.
CitationJournal: Mol.Microbiol. / Year: 2006
Title: Structural and Biochemical Characterisation of a Mitochondrial Peroxiredoxin from Plasmodium Falciparum
Authors: Boucher, I.W. / Mcmillan, P.J. / Gabrielsen, M. / Akerman, S.E. / Brannigan, J.A. / Schnick, C. / Brzozowski, A.M. / Wilkinson, A.J. / Muller, S.
History
DepositionSep 1, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2006Provider: 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 / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THIOREDOXIN PEROXIDASE 2
B: THIOREDOXIN PEROXIDASE 2


Theoretical massNumber of molelcules
Total (without water)50,5842
Polymers50,5842
Non-polymers00
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)104.632, 76.534, 60.154
Angle α, β, γ (deg.)90.00, 113.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2031-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9763, 0.04261, -0.2498), (0.04849, -0.9364, -0.3475), (-0.2488, -0.3482, 0.9038)
Vector: 39.81, 25.12, 9.922)

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Components

#1: Protein THIOREDOXIN PEROXIDASE 2 / MITOCHONDRIAL 2-CYS PEROXIREDOXIN


Mass: 25291.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: 3D7 / Plasmid: PJC40 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q9BKL4, UniProt: Q8I5Q6*PLUS, peroxidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 42.7 %
Crystal growpH: 6.5
Details: 0.2M AMMONIUM SULFATE, 0.1M BIS-TRIS 6.5, 25% PEG 3350, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 17, 2005 / Details: MIRRORS
RadiationMonochromator: SI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.78→55.22 Å / Num. obs: 41762 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.61 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.45
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 3.58 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.58 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E2Y

1e2y


Resolution: 1.78→59.87 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.768 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2106 5 %RANDOM
Rwork0.165 ---
obs0.167 39652 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å2-0.18 Å2
2--0.49 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.78→59.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2658 0 0 280 2938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222763
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9443778
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2745361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39525.417120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25715455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.293156
X-RAY DIFFRACTIONr_chiral_restr0.1150.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022078
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.21279
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21973
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2222
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.151.51775
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.922829
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.24631115
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7024.5939
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: 1.78→1.83 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.233 151
Rwork0.198 2934

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