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- PDB-1txj: Crystal structure of translationally controlled tumour-associated... -

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Basic information

Entry
Database: PDB / ID: 1txj
TitleCrystal structure of translationally controlled tumour-associated protein (TCTP) from Plasmodium knowlesi
Componentstranslationally controlled tumour-associated protein (TCTP) from Plasmodium knowlesi, PKN_PFE0545c
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Structural Genomics Consortium / SGC / guanine nucleotide-free chaperones / guanine nucleotide exchange factor / beta-sandwich / helix-turn-helix
Function / homology
Function and homology information


calcium ion binding / cytoplasm
Similarity search - Function
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 knowlesi (eukaryote)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2 Å
AuthorsWalker, J.R. / Vedadi, M. / Sharma, S. / Houston, S. / Lew, J. / Amani, M. / Wasney, G. / Skarina, T. / Bray, J. / Sundstrom, M. ...Walker, J.R. / Vedadi, M. / Sharma, S. / Houston, S. / Lew, J. / Amani, M. / Wasney, G. / Skarina, T. / Bray, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Hui, R. / Structural Genomics Consortium (SGC)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2007
Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R.
History
DepositionJul 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE THE SEQUENCE OF THE PROTEIN CAN BE FOUND IN THE PLASMODB Pk_353f04q1c.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: translationally controlled tumour-associated protein (TCTP) from Plasmodium knowlesi, PKN_PFE0545c


Theoretical massNumber of molelcules
Total (without water)19,8761
Polymers19,8761
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.633, 86.633, 55.636
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein translationally controlled tumour-associated protein (TCTP) from Plasmodium knowlesi, PKN_PFE0545c


Mass: 19876.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium knowlesi (eukaryote) / Plasmid: p11 / Production host: Escherichia coli (E. coli) / References: UniProt: P84152
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 3.31 Å3/Da / Density % sol: 62.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium citrate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 25, 2004
RadiationMonochromator: Confocal Multilayer Optics / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 16150 / Num. obs: 16150 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 54.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 8.3 / Num. unique all: 1618 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
d*TREKdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→19.86 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1173452.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 817 5.1 %RANDOM
Rwork0.199 ---
obs0.199 16129 99.6 %-
all-16129 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 83.3957 Å2 / ksol: 0.544394 e/Å3
Displacement parametersBiso mean: 40.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.72 Å23.66 Å20 Å2
2--6.72 Å20 Å2
3----13.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1294 0 0 118 1412
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it1.641.5
X-RAY DIFFRACTIONc_mcangle_it2.542
X-RAY DIFFRACTIONc_scbond_it2.332
X-RAY DIFFRACTIONc_scangle_it3.532.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.274 141 5.3 %
Rwork0.227 2522 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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