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- PDB-4o32: Structure of a malarial protein -

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Basic information

Entry
Database: PDB / ID: 4o32
TitleStructure of a malarial protein
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / protein export / malaria / protein-disulfide-reductase / parasitophorous vacuole of malarial parasite
Function / homology
Function and homology information


PTEX complex / symbiont-containing vacuole / symbiont-containing vacuole membrane / protein-disulfide reductase activity / mitochondrion / membrane / cytoplasm
Similarity search - Function
Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.196 Å
AuthorsEgea, P.F. / Koehl, A. / Peng, M. / Cascio, D.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Crystal structure and solution characterization of the thioredoxin-2 from Plasmodium falciparum, a constituent of an essential parasitic protein export complex.
Authors: Peng, M. / Cascio, D. / Egea, P.F.
History
DepositionDec 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Other
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Refinement description / Category: refine / Item: _refine.pdbx_starting_model
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin
B: Thioredoxin
C: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3874
Polymers48,3513
Non-polymers351
Water1,27971
1
A: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1522
Polymers16,1171
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)16,1171
Polymers16,1171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)16,1171
Polymers16,1171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.030, 77.030, 134.415
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Thioredoxin / / Thioredoxin-2


Mass: 16117.035 Da / Num. of mol.: 3 / Fragment: malarial thioredoxin-2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: MAL13P1.225, PF3D7_1345100, trx2 / Plasmid: pRSF / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q8IDP4
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Fragment: malarial thioredoxin-2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / Fragment: malarial thioredoxin-2 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 39.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: PEG 4000, 100 mM citrate, isopropanol 10-15%, VAPOR DIFFUSION, HANGING DROP, temperature 298K
PH range: 4.5-5.5

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97965 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2011 / Details: SI 111
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97965 Å / Relative weight: 1
ReflectionResolution: 2.196→50.642 Å / Num. all: 21370 / Num. obs: 21285 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 14.5 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 22.9

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Processing

Software
NameVersionClassification
APSdata collection
HKL2Mapmodel building
PHENIX(phenix.refine: dev_1555)refinement
XDSdata reduction
XDSdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD
Starting model: SAD derived from 3UL3

3ul3


Resolution: 2.196→50.642 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 27.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 1092 5.13 %random
Rwork0.2072 ---
obs0.2094 21273 99.55 %-
all-21285 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.196→50.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 1 71 2210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042229
X-RAY DIFFRACTIONf_angle_d0.6963013
X-RAY DIFFRACTIONf_dihedral_angle_d12.612815
X-RAY DIFFRACTIONf_chiral_restr0.027362
X-RAY DIFFRACTIONf_plane_restr0.003364
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1962-2.29610.30471350.27292429270198
2.2961-2.41720.30321260.257624862550100
2.4172-2.56860.30811500.248224722513100
2.5686-2.76690.27811320.245324902540100
2.7669-3.04530.25711390.235425132490100
3.0453-3.48590.28221250.216625402472100
3.4859-4.39150.22261480.175525502486100
4.3915-50.65530.22161370.19092701242999

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