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

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7aoo
TitlePlasmoredoxin, a redox-active protein unique for malaria parasites
ComponentsPlasmoredoxin
KeywordsOXIDOREDUCTASE / Malaria / Plasmodium falciparum / thioredoxin superfamily / redox metabolism
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) activity / protein disulfide isomerase activity / negative regulation of Wnt signaling pathway / negative regulation of protein ubiquitination / nucleus
Similarity search - Function
Thioredoxin-like / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Plasmoredoxin
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 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
B: Plasmoredoxin
C: Plasmoredoxin
D: Plasmoredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,25328
Polymers86,8834
Non-polymers3,37024
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15600 Å2
ΔGint45 kcal/mol
Surface area29520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.750, 122.730, 72.860
Angle α, β, γ (deg.)90.000, 104.881, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Plasmoredoxin


Mass: 21720.846 Da / Num. of mol.: 4
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

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Non-polymers , 5 types, 335 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium citrate pH 5.5, 40 % PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→46.26 Å / Num. obs: 106413 / % possible obs: 99.86 % / Redundancy: 4.5 % / Biso Wilson estimate: 25.61 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.05235 / Rpim(I) all: 0.027 / Rrim(I) all: 0.059 / Net I/σ(I): 13.48
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 10618 / CC1/2: 0.683 / CC star: 0.901 / Rpim(I) all: 0.467 / % possible all: 99.48

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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: 1.6→46.26 Å / SU ML: 0.1754 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.3532
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2105 5321 5 %
Rwork0.1778 101078 -
obs0.1794 106399 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.62 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5623 0 224 311 6158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01656022
X-RAY DIFFRACTIONf_angle_d1.44238059
X-RAY DIFFRACTIONf_chiral_restr0.0982804
X-RAY DIFFRACTIONf_plane_restr0.0101996
X-RAY DIFFRACTIONf_dihedral_angle_d6.24384609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.32031750.29883321X-RAY DIFFRACTION98.56
1.62-1.640.28911770.2733364X-RAY DIFFRACTION99.97
1.64-1.660.29351790.26613401X-RAY DIFFRACTION99.92
1.66-1.680.30471750.25773318X-RAY DIFFRACTION99.94
1.68-1.70.26321790.23953405X-RAY DIFFRACTION99.92
1.7-1.720.28421740.23843301X-RAY DIFFRACTION99.91
1.72-1.750.24811780.22763384X-RAY DIFFRACTION99.86
1.75-1.770.25591770.22723375X-RAY DIFFRACTION99.97
1.77-1.80.24921760.21633340X-RAY DIFFRACTION99.89
1.8-1.830.24351800.20473417X-RAY DIFFRACTION99.86
1.83-1.860.22631750.19373315X-RAY DIFFRACTION99.94
1.86-1.90.22541770.18613371X-RAY DIFFRACTION99.94
1.9-1.930.21281770.18783361X-RAY DIFFRACTION99.94
1.93-1.970.22751780.18273378X-RAY DIFFRACTION100
1.97-2.020.21381760.18063353X-RAY DIFFRACTION99.92
2.02-2.060.20361780.18213384X-RAY DIFFRACTION99.89
2.06-2.110.22791760.17963339X-RAY DIFFRACTION99.94
2.11-2.170.21691790.18073396X-RAY DIFFRACTION99.92
2.17-2.240.21411760.17623357X-RAY DIFFRACTION99.94
2.24-2.310.23151780.17973373X-RAY DIFFRACTION99.92
2.31-2.390.21171780.17643381X-RAY DIFFRACTION99.94
2.39-2.490.21541770.17553369X-RAY DIFFRACTION99.94
2.49-2.60.21341770.17643354X-RAY DIFFRACTION99.92
2.6-2.740.21591770.1773375X-RAY DIFFRACTION99.86
2.74-2.910.19371780.16743373X-RAY DIFFRACTION99.92
2.91-3.130.2041780.17533379X-RAY DIFFRACTION99.94
3.13-3.450.17681780.17223385X-RAY DIFFRACTION99.86
3.45-3.950.20051780.16243383X-RAY DIFFRACTION99.8
3.95-4.970.18121780.1473384X-RAY DIFFRACTION99.8
4.97-100.21871820.18593442X-RAY DIFFRACTION99.67

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