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- PDB-1xiy: Crystal Structure of Plasmodium falciparum antioxidant protein (1... -

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Basic information

Entry
Database: PDB / ID: 1xiy
TitleCrystal Structure of Plasmodium falciparum antioxidant protein (1-Cys peroxiredoxin)
Componentsperoxiredoxin
KeywordsOXIDOREDUCTASE / alpha-aneurysm / thioredoxin fold / peroxiredoxin fold
Function / homology
Function and homology information


peroxiredoxin / apicoplast / thioredoxin peroxidase activity / antioxidant activity / cell redox homeostasis / hydrogen peroxide catabolic process / cellular response to oxidative stress / cytoplasm
Similarity search - Function
Peroxiredoxin-5-like / Redoxin / Redoxin / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSarma, G.N. / Fischer, M. / Nickel, C. / Becker, K. / Karplus, P.A.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of a novel Plasmodium falciparum 1-Cys peroxiredoxin.
Authors: Sarma, G.N. / Nickel, C. / Rahlfs, S. / Fischer, M. / Becker, K. / Karplus, P.A.
History
DepositionSep 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 999SEQUENCE The authors state that there is an error in the database sequence.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: peroxiredoxin
B: peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)42,7202
Polymers42,7202
Non-polymers00
Water4,990277
1
A: peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)21,3601
Polymers21,3601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)21,3601
Polymers21,3601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.490, 79.770, 108.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein peroxiredoxin / / PfAOP


Mass: 21360.211 Da / Num. of mol.: 2 / Fragment: residues 60-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q5MYR6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: iso-propanol, PEG 4000, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONALS 8.2.211
SYNCHROTRONALS 8.2.121
ROTATING ANODERIGAKU RU30031.54
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJan 15, 2004
ADSC QUANTUM 42CCDNov 1, 2003
RIGAKU RAXIS IV3IMAGE PLATESep 1, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1-0.9 polarizationSINGLE WAVELENGTHMx-ray1
2-0.9 polarizationSINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.541
31
ReflectionResolution: 1.8→100 Å / Num. all: 34981 / Num. obs: 34981 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.6 %
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.5 % / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NM3

1nm3


Resolution: 1.8→100 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 3376 10 %Random
Rwork0.187 ---
all0.202 35023 --
obs0.187 33775 100 %-
Displacement parametersBiso mean: 26 Å2
Refinement stepCycle: LAST / Resolution: 1.8→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2867 0 0 277 3144
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 1.8→1.81 Å
RfactorNum. reflection% reflection
Rfree0.3011 --
Rwork0.2632 --
obs-506 10 %

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