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Yorodumi- PDB-2av4: Crystal structure of Plasmodium yoelii thioredoxin-like protein 4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2av4 | ||||||
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Title | Crystal structure of Plasmodium yoelii thioredoxin-like protein 4A (DIM1) | ||||||
Components | Thioredoxin-like protein 4A (DIM1) | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / thioredoxin-like protein / DIM1 / U5 snRNP-specific 15kD protein / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information U5 snRNP / U4/U6 x U5 tri-snRNP complex / mRNA splicing, via spliceosome Similarity search - Function | ||||||
Biological species | Plasmodium yoelii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Dong, A. / Zhao, Y. / Lew, J. / Alam, Z. / Melone, M. / Wasney, G. / Vedadi, M. / Koeieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. ...Dong, A. / Zhao, Y. / Lew, J. / Alam, Z. / Melone, M. / Wasney, G. / Vedadi, M. / Koeieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Artz, J. / 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 300 | BIOMOLECULE: 1 This entry contains the crystallographic asymmetric unit which consists of 1 chain. ...BIOMOLECULE: 1 This entry contains the crystallographic asymmetric unit which consists of 1 chain. The biological unit of the protein is not known. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2av4.cif.gz | 47.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2av4.ent.gz | 32.2 KB | Display | PDB format |
PDBx/mmJSON format | 2av4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2av4_validation.pdf.gz | 430 KB | Display | wwPDB validaton report |
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Full document | 2av4_full_validation.pdf.gz | 430.3 KB | Display | |
Data in XML | 2av4_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 2av4_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/2av4 ftp://data.pdbj.org/pub/pdb/validation_reports/av/2av4 | HTTPS FTP |
-Related structure data
Related structure data | 1txjC 1xccC 1y6zC 1z6gC 1z7dC 1z81C 1zo2C 2a22C 2a4aC 2aifC 2amxC 2aqwC 2awpC 2ayvC 2b71C 2bddC 2f4zC 2fdsC 2ffcC 2fo3C 2fu0C 2ghiC 2h1rC 2h2yC 2h66C 2hjrC 2hteC 2hvgC 3pggC 3tb2C 1qgvS S: Starting model for refinement 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18696.314 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium yoelii (eukaryote) / Gene: PY07357 / Plasmid: pET28aLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q7R866 | ||
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#2: Chemical | ChemComp-CL / #3: 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: 2.6 Å3/Da / Density % sol: 53.2 % |
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Crystal grow | Temperature: 295 K Details: 1.4 M NaCl, pH 9.0, VAPOR DIFFUSION, temperature 295 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.99998 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 12, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99998 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→41.5 Å / Num. all: 20820 / Num. obs: 20820 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.73→1.86 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 2.28 / Rsym value: 0.385 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QGV Resolution: 1.73→41.5 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.783 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.552 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→41.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.728→1.773 Å / Total num. of bins used: 20
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