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- PDB-7u2v: Plasmodium falciparum Cyt c2 DSD -

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Basic information

Entry
Database: PDB / ID: 7u2v
TitlePlasmodium falciparum Cyt c2 DSD
ComponentsCytochrome c2
KeywordsELECTRON TRANSPORT / alpha helix / heme / DSD / domain-swapped dimer
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Transcriptional activation of mitochondrial biogenesis / Detoxification of Reactive Oxygen Species / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial intermembrane space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / Cytochrome c, putative
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å
Model detailsPlasmodium falciparum Cyt c2 forming a domain-swapped dimer complex
AuthorsHill, C.P. / Wienkers, H.J. / Whitby, F.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133764 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Direct tests of cytochrome c and c1 functions in the electron transport chain of malaria parasites
Authors: Espino-Sanchez, T.J. / Wienkers, H. / Marvin, R.G. / Nalder, S.A. / Garcia-Guerrero, A.E. / VanNatta, P.E. / Jami-Alahmadi, Y. / Mixon Blackwell, A. / Whitby, F.G. / Wohlschlegel, J.A. / ...Authors: Espino-Sanchez, T.J. / Wienkers, H. / Marvin, R.G. / Nalder, S.A. / Garcia-Guerrero, A.E. / VanNatta, P.E. / Jami-Alahmadi, Y. / Mixon Blackwell, A. / Whitby, F.G. / Wohlschlegel, J.A. / Kieber-Emmons, M.T. / Hill, C.P. / Sigala, P.A.
History
DepositionFeb 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c2
B: Cytochrome c2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2184
Polymers35,9812
Non-polymers1,2372
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9240 Å2
ΔGint-112 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.846, 54.613, 71.464
Angle α, β, γ (deg.)90.000, 102.190, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome c2


Mass: 17990.361 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_1311700 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8I6T6
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M sodium chloride, 0.1 M Bis-Tris, pH 5.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 1.73816 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.73816 Å / Relative weight: 1
ReflectionResolution: 2.55→39.92 Å / Num. obs: 8552 / % possible obs: 84.2 % / Redundancy: 47.6 % / Biso Wilson estimate: 5.8 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.41 / Rpim(I) all: 0.064 / Rrim(I) all: 0.416 / Net I/σ(I): 20.2 / Num. measured all: 407151 / Scaling rejects: 2777
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.55-2.6629.13.162120834150.8920.6093.223835.1
8.83-39.9248.70.095125212570.9980.0130.09628.597

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
SOLVEphasing
RESOLVEmodel building
PHENIX1.19.2-4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.55→39.92 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 851 10 %
Rwork0.1893 7658 -
obs0.1948 8509 83.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.86 Å2 / Biso mean: 25.3151 Å2 / Biso min: 0.89 Å2
Refinement stepCycle: final / Resolution: 2.55→39.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1825 0 146 6 1977
Biso mean--11.27 12.39 -
Num. residues----226
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.710.2634650.195358364839
2.71-2.920.29371190.19581039115869
2.92-3.210.23971590.20511465162497
3.22-3.680.24361640.18671507167199
3.68-4.630.21141690.16831525169499
4.64-39.920.2521750.20061539171499
Refinement TLS params.Method: refined / Origin x: 0.0926 Å / Origin y: 21.8733 Å / Origin z: 18.6359 Å
111213212223313233
T0.0573 Å20.0118 Å20.0158 Å2--0.2208 Å20.1419 Å2---0.1052 Å2
L0.2203 °2-0.0791 °20.0854 °2-0.523 °20.2533 °2--0.2112 °2
S-0.0174 Å °0.1051 Å °0.0792 Å °-0.3403 Å °-0.0515 Å °-0.0529 Å °-0.151 Å °0.0694 Å °-0.6885 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA20 - 231
2X-RAY DIFFRACTION1allB20 - 231
3X-RAY DIFFRACTION1allC1 - 6

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