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Yorodumi- PDB-2wei: Crystal structure of the kinase domain of Cryptosporidium parvum ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wei | ||||||
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Title | Crystal structure of the kinase domain of Cryptosporidium parvum calcium dependent protein kinase in complex with 3-MB-PP1 | ||||||
Components | CALMODULIN-DOMAIN PROTEIN KINASE 1, PUTATIVE | ||||||
Keywords | TRANSFERASE / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / KINASE / ATP-BINDING | ||||||
Function / homology | Function and homology information calcium-dependent protein serine/threonine kinase activity / calcium/calmodulin-dependent protein kinase activity / calmodulin binding / intracellular signal transduction / calcium ion binding / ATP binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | CRYPTOSPORIDIUM PARVUM IOWA II (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Roos, A.K. / King, O. / Chaikuad, A. / Zhang, C. / Shokat, K.M. / Wernimont, A.K. / Artz, J.D. / Lin, L. / MacKenzie, F.I. / Finerty, P.J. ...Roos, A.K. / King, O. / Chaikuad, A. / Zhang, C. / Shokat, K.M. / Wernimont, A.K. / Artz, J.D. / Lin, L. / MacKenzie, F.I. / Finerty, P.J. / Vedadi, M. / Schapira, M. / Indarte, M. / Kozieradzki, I. / Pike, A.C.W. / Fedorov, O. / Doyle, D. / Muniz, J. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / von Delft, F. / Heightman, T. / Hui, R. | ||||||
Citation | Journal: Bmc Genomics / Year: 2011 Title: The Cryptosporidium Parvum Kinome. Authors: Artz, J.D. / Wernimont, A.K. / Allali-Hassani, A. / Zhao, Y. / Amani, M. / Lin, Y.H. / Senisterra, G. / Wasney, G.A. / Fedorov, O. / King, O. / Roos, A.K. / Lunin, V.V. / Qiu, W. / Finerty, ...Authors: Artz, J.D. / Wernimont, A.K. / Allali-Hassani, A. / Zhao, Y. / Amani, M. / Lin, Y.H. / Senisterra, G. / Wasney, G.A. / Fedorov, O. / King, O. / Roos, A.K. / Lunin, V.V. / Qiu, W. / Finerty, P.J. / Hutchinson, A. / Chau, I. / von Delft, F. / MacKenzie, F.I. / Lew, J. / Kozieradzki, I. / Vedadi, M. / Schapira, M. / Zhang, C. / Shokat, K.M. / Heightman, T. / Hui, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wei.cif.gz | 76.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wei.ent.gz | 56 KB | Display | PDB format |
PDBx/mmJSON format | 2wei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wei_validation.pdf.gz | 744.1 KB | Display | wwPDB validaton report |
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Full document | 2wei_full_validation.pdf.gz | 745.5 KB | Display | |
Data in XML | 2wei_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 2wei_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/2wei ftp://data.pdbj.org/pub/pdb/validation_reports/we/2wei | HTTPS FTP |
-Related structure data
Related structure data | 3dfaS S: Starting model for refinement |
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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: 33445.398 Da / Num. of mol.: 1 / Fragment: RESIDUES 70-338 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CRYPTOSPORIDIUM PARVUM IOWA II (eukaryote) Gene: CGD3_920 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3PACYC-LIC LAMP-PHOSPHATASE / References: UniProt: A3FQ16, xylulokinase |
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#2: Chemical | ChemComp-VGG / |
#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: 2.33 Å3/Da / Density % sol: 47.18 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: 25% PEG 3350, 0.1M BIS-TRIS PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99989 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99989 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→32.62 Å / Num. obs: 38607 / % possible obs: 99.9 % / Observed criterion σ(I): 2.3 / Redundancy: 8.3 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 7 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DFA Resolution: 1.65→33.5 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.197 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
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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: 9.927 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→33.5 Å
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Refine LS restraints |
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