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- PDB-9k2l: Crystal structure of Plasmoredoxin, a disulfide oxidoreductase fr... -

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Basic information

Entry
Database: PDB / ID: 9k2l
TitleCrystal structure of Plasmoredoxin, a disulfide oxidoreductase from Plasmodium falciparum crystallized in the presence of Glutathione(GSH)
ComponentsPlasmoredoxin
KeywordsOXIDOREDUCTASE / Plasmodium falciparum / GSH
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: 1.4 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 Glutathione(GSH)
Authors: Panicker, L.
History
DepositionOct 17, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

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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)26,0852
Polymers25,9891
Non-polymers961
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-6 kcal/mol
Surface area9850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.162, 50.348, 77.888
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
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_0303600
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8I224
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.85 Å3/Da / Density % sol: 33.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium acetate, ammonium sulphate, PEG 8000 , 5mM GSH

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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: 1.4→49.16 Å / Num. obs: 37724 / % possible obs: 97.5 % / Redundancy: 15.1 % / Biso Wilson estimate: 10.42 Å2 / CC1/2: 0.999 / Net I/σ(I): 24.4
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 1400 / CC1/2: 0.731

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→41.57 Å / SU ML: 0.1296 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.7678
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2098 1571 4.99 %
Rwork0.1732 35758 -
obs0.175 37637 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.17 Å2
Refinement stepCycle: LAST / Resolution: 1.4→41.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 5 108 1571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561507
X-RAY DIFFRACTIONf_angle_d0.77982038
X-RAY DIFFRACTIONf_chiral_restr0.0837207
X-RAY DIFFRACTIONf_plane_restr0.008256
X-RAY DIFFRACTIONf_dihedral_angle_d5.5595189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.24981160.19922153X-RAY DIFFRACTION77.44
1.44-1.480.23671440.1812451X-RAY DIFFRACTION89.08
1.48-1.530.25441490.17642732X-RAY DIFFRACTION97.76
1.53-1.580.21091470.16732776X-RAY DIFFRACTION99.8
1.58-1.650.23171480.16352798X-RAY DIFFRACTION100
1.65-1.720.18661670.16122778X-RAY DIFFRACTION99.9
1.72-1.810.21381690.16352795X-RAY DIFFRACTION100
1.81-1.930.21321330.15682820X-RAY DIFFRACTION100
1.93-2.070.19121150.15882856X-RAY DIFFRACTION100
2.07-2.280.17041570.16652839X-RAY DIFFRACTION100
2.28-2.610.23391590.17972843X-RAY DIFFRACTION99.97
2.61-3.290.2491390.19322898X-RAY DIFFRACTION99.97
3.29-41.570.18051360.17283019X-RAY DIFFRACTION99.28

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