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- PDB-7aoj: Plasmoredoxin, a redox-active protein unique for malaria parasites -

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Basic information

Entry
Database: PDB / ID: 7aoj
TitlePlasmoredoxin, a redox-active protein unique for malaria parasites
ComponentsPlasmoredoxin
KeywordsOXIDOREDUCTASE / Malaria / Plasmodium falciparum / thioredoxin superfamily / redox metabolism
Function / homologyThioredoxin-like / Thioredoxin-like fold / thioredoxin-disulfide reductase (NADPH) activity / protein disulfide isomerase activity / negative regulation of Wnt signaling pathway / negative regulation of protein ubiquitination / Thioredoxin-like superfamily / nucleus / Plasmoredoxin
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.63 Å
AuthorsFritz-Wolf, K. / Bathke, J. / Rahlfs, S. / Becker, K.
Funding support1items
OrganizationGrant numberCountry
Hessian Ministry of Science, Higher Education and Art (HMWK)
CitationJournal: Curr Res Struct Biol / Year: 2022
Title: Crystal structure of plasmoredoxin, a redox-active protein unique for malaria parasites.
Authors: Fritz-Wolf, K. / Bathke, J. / Rahlfs, S. / Becker, K.
History
DepositionOct 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasmoredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1816
Polymers21,7211
Non-polymers4605
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-3 kcal/mol
Surface area8960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.000, 74.000, 65.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Plasmoredoxin


Mass: 21720.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_0303600 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8I224
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1,6 ammonium sulfate, 0.5 M glycine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.63→19.45 Å / Num. obs: 25144 / % possible obs: 99.16 % / Redundancy: 9.9 % / Biso Wilson estimate: 19.86 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.0155 / Rrim(I) all: 0.0593 / Rsym value: 0.057 / Net I/σ(I): 33.87
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.3433 / Mean I/σ(I) obs: 4 / Num. unique obs: 2336 / CC1/2: 0.87 / CC star: 0.965 / Rpim(I) all: 0.1802 / Rrim(I) all: 0.3908 / Rsym value: 0.339 / % possible all: 92.23

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.63→19.45 Å / SU ML: 0.1597 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.5279
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1997 1258 5 %Random selection
Rwork0.1682 23886 --
obs0.1698 25144 99.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.95 Å2
Refinement stepCycle: LAST / Resolution: 1.63→19.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1371 0 30 149 1550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01711461
X-RAY DIFFRACTIONf_angle_d1.48481969
X-RAY DIFFRACTIONf_chiral_restr0.1198
X-RAY DIFFRACTIONf_plane_restr0.0106245
X-RAY DIFFRACTIONf_dihedral_angle_d6.40341196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.70.24651310.21182473X-RAY DIFFRACTION92.97
1.7-1.770.23381400.20142666X-RAY DIFFRACTION100
1.77-1.870.22271400.1942660X-RAY DIFFRACTION100
1.87-1.980.21881400.18222654X-RAY DIFFRACTION100
1.98-2.140.22371400.17392670X-RAY DIFFRACTION100
2.14-2.350.21821410.172671X-RAY DIFFRACTION100
2.35-2.690.21481410.17632680X-RAY DIFFRACTION100
2.69-3.390.18241410.16652692X-RAY DIFFRACTION100
3.39-19.450.17791440.14932720X-RAY DIFFRACTION99.97

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