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- PDB-9khr: Crystal structure of Plasmoredoxin, a disulfide oxidoreductase fr... -

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Basic information

Entry
Database: PDB / ID: 9khr
TitleCrystal structure of Plasmoredoxin, a disulfide oxidoreductase from Plasmodium falciparum crystallized in the presence of Dithiothreitol (DTT)
ComponentsPlasmoredoxin
KeywordsOXIDOREDUCTASE / Plasmodium falciparum / DTT
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 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPanicker, L.
Funding support India, 1items
OrganizationGrant numberCountry
Other governmentNA India
CitationJournal: To Be Published
Title: Crystal structure of Plasmoredoxin, a disulfide oxidoreductase from Plasmodium falciparum crystallized in the presence of Dithiothreitol (DTT)
Authors: Panicker, L.
History
DepositionNov 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plasmoredoxin


Theoretical massNumber of molelcules
Total (without water)25,9891
Polymers25,9891
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.704, 50.310, 78.018
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Plasmoredoxin


Mass: 25988.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Plasmoredoxin an oxidoreductase protein fromPlasmodium Falciparum
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_0303600
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8I224
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 1.84 Å3/Da / Density % sol: 33.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium acetate, ammonium sulphate, PEG 8000 , 5mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9789 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2→42.28 Å / Num. obs: 13487 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 16.44 Å2 / CC1/2: 0.996 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 963 / CC1/2: 0.918

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9JQ9

9jq9


Resolution: 2→41.31 Å / SU ML: 0.104 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.0707
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2346 621 4.67 %
Rwork0.2061 12671 -
obs0.2075 13292 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.75 Å2
Refinement stepCycle: LAST / Resolution: 2→41.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 0 0 61 1527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00761511
X-RAY DIFFRACTIONf_angle_d0.82842043
X-RAY DIFFRACTIONf_chiral_restr0.054208
X-RAY DIFFRACTIONf_plane_restr0.0072258
X-RAY DIFFRACTIONf_dihedral_angle_d5.821190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.20.22471370.19293090X-RAY DIFFRACTION97.88
2.2-2.520.24181500.20583106X-RAY DIFFRACTION98.25
2.52-3.180.26381610.23023191X-RAY DIFFRACTION99.91
3.18-41.310.21931730.19743284X-RAY DIFFRACTION98.74

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