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Yorodumi- PDB-2jam: Crystal structure of human calmodulin-dependent protein kinase I G -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jam | ||||||
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Title | Crystal structure of human calmodulin-dependent protein kinase I G | ||||||
Components |
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Keywords | TRANSFERASE / KINASE / MEMBRANE / ATP-BINDING / PRENYLATION / SERINE/THREONINE-PROTEIN KINASE / ALTERNATIVE SPLICING / PROTEIN SERINE/THREONINE KINASE / CALMODULIN BINDING / CALMODULIN-BINDING / NUCLEOTIDE BINDING / NUCLEOTIDE-BINDING / LIPOPROTEIN / POLYMORPHISM / GOLGI APPARATUS / PHOSPHORYLATION / ALLOSTERIC ENZYME | ||||||
Function / homology | Function and homology information calcium- and calmodulin-dependent protein kinase complex / Ca2+/calmodulin-dependent protein kinase / calmodulin-dependent protein kinase activity / peptidyl-serine phosphorylation / calmodulin binding / neuron projection / Golgi membrane / protein serine/threonine kinase activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) UNIDENTIFIED (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Debreczeni, J.E. / Bullock, A. / Keates, T. / Niesen, F.H. / Salah, E. / Shrestha, L. / Smee, C. / Sobott, F. / Pike, A.C.W. / Bunkoczi, G. ...Debreczeni, J.E. / Bullock, A. / Keates, T. / Niesen, F.H. / Salah, E. / Shrestha, L. / Smee, C. / Sobott, F. / Pike, A.C.W. / Bunkoczi, G. / von Delft, F. / Turnbull, A. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Knapp, S. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Human Calmodulin-Dependent Protein Kinase I G Authors: Debreczeni, J.E. / Bullock, A. / Keates, T. / Niesen, F.H. / Salah, E. / Shrestha, L. / Smee, C. / Sobott, F. / Pike, A.C.W. / Bunkoczi, G. / von Delft, F. / Turnbull, A. / Weigelt, J. / ...Authors: Debreczeni, J.E. / Bullock, A. / Keates, T. / Niesen, F.H. / Salah, E. / Shrestha, L. / Smee, C. / Sobott, F. / Pike, A.C.W. / Bunkoczi, G. / von Delft, F. / Turnbull, A. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jam.cif.gz | 256.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jam.ent.gz | 204.4 KB | Display | PDB format |
PDBx/mmJSON format | 2jam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/2jam ftp://data.pdbj.org/pub/pdb/validation_reports/ja/2jam | HTTPS FTP |
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-Related structure data
Related structure data | 1a06S 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.31581, -0.39779, 0.86141), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34805.852 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 18-316 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): R3 ROSETTA References: UniProt: Q96NX5, Ca2+/calmodulin-dependent protein kinase |
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-Protein/peptide , 2 types, 2 molecules DE
#2: Protein/peptide | Mass: 608.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UNKNOWN ORIGIN / Source: (natural) UNIDENTIFIED (others) |
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#3: Protein/peptide | Mass: 480.577 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UNKNOWN ORIGIN / Source: (natural) UNIDENTIFIED (others) |
-Non-polymers , 4 types, 326 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CA / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE PEPTIDES CORRESPONDING TO CHAINS D AND E ARE OF UNKNOWN ORIGIN, I.E. THEY WERE NOT PART OF THE ...THE PEPTIDES CORRESPOND |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45 % |
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Crystal grow | Details: 0.20M NA(MALONATE), 0.1M BTPROP PH 7.5, 20.0% PEG 3350, 10.0% ETGLY |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 19, 2006 / Details: MIRRORS |
Radiation | Monochromator: SI 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→33.36 Å / Num. obs: 64017 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 2.79 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.82 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 2.31 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.97 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A06 Resolution: 1.7→56.89 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.166 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.112 / 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: 19.66 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→56.89 Å
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Refine LS restraints |
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