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Yorodumi- PDB-1txj: Crystal structure of translationally controlled tumour-associated... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1txj | ||||||
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Title | Crystal structure of translationally controlled tumour-associated protein (TCTP) from Plasmodium knowlesi | ||||||
Components | translationally controlled tumour-associated protein (TCTP) from Plasmodium knowlesi, PKN_PFE0545c | ||||||
Keywords | STRUCTURAL 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 | ||||||
Biological species | Plasmodium knowlesi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 2 Å | ||||||
Authors | Walker, 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) | ||||||
Citation | Journal: 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 |
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Remark 999 | SEQUENCE THE SEQUENCE OF THE PROTEIN CAN BE FOUND IN THE PLASMODB Pk_353f04q1c. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1txj.cif.gz | 46.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1txj.ent.gz | 33.4 KB | Display | PDB format |
PDBx/mmJSON format | 1txj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/1txj ftp://data.pdbj.org/pub/pdb/validation_reports/tx/1txj | HTTPS FTP |
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-Related structure data
Related structure data | 1xccC 1y6zC 1z6gC 1z7dC 1z81C 1zo2C 2a22C 2a4aC 2aifC 2amxC 2aqwC 2av4C 2awpC 2ayvC 2b71C 2bddC 2f4zC 2fdsC 2ffcC 2fo3C 2fu0C 2ghiC 2h1rC 2h2yC 2h66C 2hjrC 2hteC 2hvgC 3pggC 3tb2C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.83 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: sodium citrate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 25, 2004 |
Radiation | Monochromator: Confocal Multilayer Optics / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 83.3957 Å2 / ksol: 0.544394 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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