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- PDB-9jq9: Crystal structure of Plasmoredoxin from Plasmodium falciparum a d... -

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Basic information

Entry
Database: PDB / ID: 9jq9
TitleCrystal structure of Plasmoredoxin from Plasmodium falciparum a disulfide oxidoreductase protein unique to Plasmodium species
ComponentsPlasmoredoxin
KeywordsOXIDOREDUCTASE
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: 1.9 Å
AuthorsPanicker, L.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)barc India
CitationJournal: To Be Published
Title: Crystal structure of Plasmoredoxin from Plasmodium falciparum a disulfide oxidoreductase protein unique to Plasmodium species
Authors: Panicker, L.
History
DepositionSep 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 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


Theoretical massNumber of molelcules
Total (without water)21,7211
Polymers21,7211
Non-polymers00
Water1,08160
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)48.551, 50.499, 78.571
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: 21720.846 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: ammonium acetate, ammonium sulphate, PEG-8000

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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 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.36 Å / Relative weight: 1
ReflectionResolution: 1.9→41.3 Å / Num. obs: 15673 / % possible obs: 99.43 % / Redundancy: 11.6 % / Biso Wilson estimate: 22.05 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06169 / Rpim(I) all: 0.01791 / Rrim(I) all: 0.0644 / Net I/σ(I): 26.25
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.4582 / Mean I/σ(I) obs: 3.77 / Num. unique obs: 1517 / CC1/2: 0.957 / CC star: 0.989 / Rpim(I) all: 0.1798 / Rrim(I) all: 0.4582 / % possible all: 98.25

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→41.3 Å / SU ML: 0.2387 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1109
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: refined with phenix-refine
RfactorNum. reflection% reflection
Rfree0.2367 777 4.96 %
Rwork0.2041 14890 -
obs0.2058 15667 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.35 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1429 0 0 60 1489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091472
X-RAY DIFFRACTIONf_angle_d0.93511990
X-RAY DIFFRACTIONf_chiral_restr0.0575203
X-RAY DIFFRACTIONf_plane_restr0.0094251
X-RAY DIFFRACTIONf_dihedral_angle_d6.0825186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.020.30371230.25152426X-RAY DIFFRACTION98.65
2.02-2.180.2411450.20412413X-RAY DIFFRACTION99.65
2.18-2.40.25211050.21042475X-RAY DIFFRACTION99.35
2.4-2.740.27181250.21142465X-RAY DIFFRACTION99.65
2.74-3.460.26021450.2162493X-RAY DIFFRACTION99.85
3.46-100.19391340.18352618X-RAY DIFFRACTION99.53

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