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- PDB-9k98: Crystal structure of Plasmoredoxin, a disulfide oxidoreductase fr... -

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Basic information

Entry
Database: PDB / ID: 9k98
TitleCrystal structure of Plasmoredoxin, a disulfide oxidoreductase from Plasmodium falciparum
ComponentsPlasmoredoxin
KeywordsOXIDOREDUCTASE / Plasmoredoxin / disulfide oxidoreductase / Plasmodium falciparum
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 / MOLECULAR REPLACEMENT / Resolution: 1.77 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
Authors: Panicker, L.
History
DepositionOct 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: 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
Water66737
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.220, 74.220, 63.503
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: 25988.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Plasmoredoxin an oxidoreductase protein from Plasmodium 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.: 37 / 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: 1.94 Å3/Da / Density % sol: 36.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: Excillum MetalJet D2+ 160 kV / Wavelength: 1.36 Å
DetectorType: DECTRIS PILATUS3 R 1M / Detector: PIXEL / Date: Sep 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.36 Å / Relative weight: 1
ReflectionResolution: 1.77→45.17 Å / Num. obs: 18822 / % possible obs: 96.7 % / Redundancy: 15.7 % / Biso Wilson estimate: 25.63 Å2 / CC1/2: 1 / Net I/σ(I): 34.1
Reflection shellResolution: 1.77→1.81 Å / Num. unique obs: 579 / CC1/2: 0.962

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→45.17 Å / SU ML: 0.2473 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.4089
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2585 932 4.97 %
Rwork0.2253 17834 -
obs0.227 18766 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.64 Å2
Refinement stepCycle: LAST / Resolution: 1.77→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1345 0 0 37 1382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791386
X-RAY DIFFRACTIONf_angle_d0.90951875
X-RAY DIFFRACTIONf_chiral_restr0.0641192
X-RAY DIFFRACTIONf_plane_restr0.0075237
X-RAY DIFFRACTIONf_dihedral_angle_d9.0167175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.860.34671050.27132031X-RAY DIFFRACTION77.84
1.86-1.980.32261190.29552613X-RAY DIFFRACTION98.91
1.98-2.130.32911430.25742614X-RAY DIFFRACTION99.89
2.13-2.350.30121460.24572619X-RAY DIFFRACTION99.82
2.35-2.690.29431250.25312644X-RAY DIFFRACTION99.96
2.69-3.390.26241480.24892635X-RAY DIFFRACTION100
3.39-45.170.20851460.17842678X-RAY DIFFRACTION99.93

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