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Yorodumi- PDB-6of9: Structure of the Chlamydamonas reinhardtii CamKII hub homology domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 6of9 | |||||||||
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Title | Structure of the Chlamydamonas reinhardtii CamKII hub homology domain | |||||||||
Components | CaMKII hub | |||||||||
Keywords | UNKNOWN FUNCTION / Chlamydomonas reinhardtii CaMKII hub domain homolog | |||||||||
Function / homology | Function and homology information calcium/calmodulin-dependent protein kinase activity / calmodulin binding Similarity search - Function | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | McSpadden, E.D. / Chi, C.C. / Gee, C.L. / Kuriyan, J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Protein Sci. / Year: 2019 Title: Variation in assembly stoichiometry in non-metazoan homologs of the hub domain of Ca2+/calmodulin-dependent protein kinase II. Authors: McSpadden, E.D. / Xia, Z. / Chi, C.C. / Susa, A.C. / Shah, N.H. / Gee, C.L. / Williams, E.R. / Kuriyan, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6of9.cif.gz | 232.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6of9.ent.gz | 190.1 KB | Display | PDB format |
PDBx/mmJSON format | 6of9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6of9_validation.pdf.gz | 250 KB | Display | wwPDB validaton report |
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Full document | 6of9_full_validation.pdf.gz | 250 KB | Display | |
Data in XML | 6of9_validation.xml.gz | 919 B | Display | |
Data in CIF | 6of9_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/6of9 ftp://data.pdbj.org/pub/pdb/validation_reports/of/6of9 | HTTPS FTP |
-Related structure data
Related structure data | 6of8C 1hkxS 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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Unit cell |
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-Components
#1: Protein | Mass: 14801.037 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLREDRAFT_156470 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8IHL6, UniProt: A0A2K3DJN8*PLUS #2: Water | ChemComp-HOH / | |
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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: 5.59 Å3/Da / Density % sol: 77.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.15 M DL-Malic acid (pH 7.0), 20% (w/v) polyethylene glycol 3350 precipitant. Protein 15 mg/ml in 16 mM tris, 96 mM KCl, 6.4 mM imidazole, 0.64 mM DTT, 6.4% glycerol pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2016 | |||||||||||||||||||||||||||
Radiation | Monochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.11583 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 3→49.04 Å / Num. obs: 61612 / % possible obs: 100 % / Redundancy: 7.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.11 / Rrim(I) all: 0.219 / Net I/av σ(I): 10 / Net I/σ(I): 10 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HKX Resolution: 3→49.042 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0.11 / Phase error: 25.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→49.042 Å
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Refine LS restraints |
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LS refinement shell |
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