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Yorodumi- PDB-3byv: Crystal structure of Toxoplasma gondii specific rhoptry antigen k... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3byv | ||||||
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Title | Crystal structure of Toxoplasma gondii specific rhoptry antigen kinase domain | ||||||
Components | Rhoptry kinase | ||||||
Keywords | TRANSFERASE / toxoplasma / 33.m00005 / rhoptry / malaria / kinase / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Wernimont, A.K. / Lunin, V.V. / Yang, C. / Lew, J. / Kozieradzki, I. / Lin, Y.H. / Sun, X. / Khuu, C. / Zhao, Y. / Schapira, M. ...Wernimont, A.K. / Lunin, V.V. / Yang, C. / Lew, J. / Kozieradzki, I. / Lin, Y.H. / Sun, X. / Khuu, C. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bochkarev, A. / Hui, R. / Sibley, D. / Qiu, W. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Embo J. / Year: 2009 Title: Novel structural and regulatory features of rhoptry secretory kinases in Toxoplasma gondii. Authors: Qiu, W. / Wernimont, A. / Tang, K. / Taylor, S. / Lunin, V. / Schapira, M. / Fentress, S. / Hui, R. / Sibley, L.D. | ||||||
History |
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Remark 999 | SEQUENCE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE ... SEQUENCE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3byv.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3byv.ent.gz | 68 KB | Display | PDB format |
PDBx/mmJSON format | 3byv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/3byv ftp://data.pdbj.org/pub/pdb/validation_reports/by/3byv | HTTPS FTP |
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-Related 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: 43774.082 Da / Num. of mol.: 1 / Fragment: Residues 210-568 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: 33.m00005 / Production host: Escherichia coli (E. coli) / References: UniProt: O15693*PLUS | ||
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#2: Chemical | ChemComp-MG / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal |
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Crystal grow |
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.8→40 Å / Num. all: 33484 / Num. obs: 33484 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.06 / Net I/σ(I): 28.5 | |||||||||||||||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 4.21 / Num. unique all: 3306 / Rsym value: 0.427 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→36.44 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.484 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.132 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.045 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→36.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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