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- PDB-3p3k: The crystal structure of translationally controlled tumor protein... -

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Basic information

Entry
Database: PDB / ID: 3p3k
TitleThe crystal structure of translationally controlled tumor protein (TCTP) of Plasmodium falciparum
ComponentsTranslationally-controlled tumor protein homolog
KeywordsMETAL BINDING PROTEIN / Mainly Beta
Function / homology
Function and homology information


food vacuole / calcium ion binding / cytoplasm
Similarity search - Function
Translationally controlled tumour protein, conserved site / Translationally controlled tumor protein (TCTP) domain signature 2. / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Translationally controlled tumour protein / Translationally controlled tumour protein (TCTP) domain / Translationally controlled tumour protein / Translationally controlled tumor protein (TCTP) domain profile. / Mss4/translationally controlled tumour-associated TCTP / Mss4-like superfamily / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A ...Translationally controlled tumour protein, conserved site / Translationally controlled tumor protein (TCTP) domain signature 2. / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Translationally controlled tumour protein / Translationally controlled tumour protein (TCTP) domain / Translationally controlled tumour protein / Translationally controlled tumor protein (TCTP) domain profile. / Mss4/translationally controlled tumour-associated TCTP / Mss4-like superfamily / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Translationally-controlled tumor protein homolog
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.551 Å
AuthorsEichhorn, T. / Winter, D. / Dirdjaja, N. / Frank, M. / Krauth-Siegel, L. / Granzin, J. / Efferth, T.
CitationJournal: Biochem Pharmacol / Year: 2013
Title: Molecular interaction of artemisinin with translationally controlled tumor protein (TCTP) of Plasmodium falciparum.
Authors: Eichhorn, T. / Winter, D. / Buchele, B. / Dirdjaja, N. / Frank, M. / Lehmann, W.D. / Mertens, R. / Krauth-Siegel, R.L. / Simmet, T. / Granzin, J. / Efferth, T.
History
DepositionOct 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Jan 9, 2013Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Translationally-controlled tumor protein homolog


Theoretical massNumber of molelcules
Total (without water)21,6381
Polymers21,6381
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.858, 61.858, 111.684
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 Translationally-controlled tumor protein homolog / TCTP


Mass: 21638.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: TCTP, PFE0545c / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I3Z5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 21.5 % PEG 4000, 1,6-hexanediol, 50 mM bis-tris methane, 50mM magnesium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 5, 2009 / Details: Graphite Monochromator
RadiationMonochromator: Graphite Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→29.8 Å / Num. obs: 7436 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Biso Wilson estimate: 50.1 Å2 / Rmerge(I) obs: 0.056
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 7.6 / % possible all: 98.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TXJ

1txj


Resolution: 2.551→29.8 Å / SU ML: 0.4 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2402 342 4.6 %RANDOM
Rwork0.2157 ---
obs0.2169 7436 98.53 %-
all-7455 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.14 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1--3.2733 Å2-0 Å20 Å2
2---3.2733 Å20 Å2
3---6.5465 Å2
Refinement stepCycle: LAST / Resolution: 2.551→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 0 66 1418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021388
X-RAY DIFFRACTIONf_angle_d0.5891863
X-RAY DIFFRACTIONf_dihedral_angle_d12.603520
X-RAY DIFFRACTIONf_chiral_restr0.046190
X-RAY DIFFRACTIONf_plane_restr0.001238
LS refinement shell
Resolution (Å)Num. reflection RfreeNum. reflection RworkRefine-IDNum. reflection obs% reflection obs (%)
2.5506-3.21291593450X-RAY DIFFRACTION345098
3.2129-29.8091833644X-RAY DIFFRACTION364499

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