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Yorodumi- PDB-3h51: Crystal structure of Putative calcium/calmodulin dependent protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h51 | ||||||
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Title | Crystal structure of Putative calcium/calmodulin dependent protein kinase II association domain (NP_636218.1) from XANTHOMONAS CAMPESTRIS at 1.70 A resolution | ||||||
Components | Putative calcium/calmodulin dependent protein kinase II association domain | ||||||
Keywords | PROTEIN BINDING / NP_636218.1 / Putative calcium/calmodulin dependent protein kinase II association domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / unknown function | ||||||
Function / homology | Function and homology information calcium/calmodulin-dependent protein kinase activity / calmodulin binding Similarity search - Function | ||||||
Biological species | Xanthomonas campestris pv. campestris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Putative calcium/calmodulin dependent protein kinase II association domain (NP_636218.1) from XANTHOMONAS CAMPESTRIS at 1.70 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h51.cif.gz | 76.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h51.ent.gz | 59.4 KB | Display | PDB format |
PDBx/mmJSON format | 3h51.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h51_validation.pdf.gz | 457.8 KB | Display | wwPDB validaton report |
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Full document | 3h51_full_validation.pdf.gz | 462.6 KB | Display | |
Data in XML | 3h51_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 3h51_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/3h51 ftp://data.pdbj.org/pub/pdb/validation_reports/h5/3h51 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Details | ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. |
-Components
#1: Protein | Mass: 17258.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria) Gene: NP_636218.1, XCC0827 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8PCA7 #2: Chemical | Num. of mol.: 2 / Source method: obtained synthetically #3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (RESIDUES 20-174) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 20-174) WAS EXPRESSED WITH A PURIFICATI | |
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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: 2.32 Å3/Da / Density % sol: 46.96 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20.0000% PEG-1000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97901 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 18, 2009 / Details: Flat mirror (vertical focusing) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→29.488 Å / Num. obs: 33865 / % possible obs: 97.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 22.186 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 6.464 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→29.488 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 4.425 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.107 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. PEG AND PG4 MOLECULES (FRAGMENTS OF PEG1000 AND PEG200) USED IN THE CRYSTALLIZATION AND CRYOPROTECTION CONDITION HAVE BEEN MODELED. 5. ELECTRON DENSITIES OF RESIDUES OF 30-34 AND 108-112 IN BOTH A AND B CHAINS ARE POOR AND MODELS ARE NOT RELIABLE IN THIS REGION. 6. AN UNIDENTIFIED LIGAND (UNL) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE OF BOTH A AND B CHAINS.
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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 max: 65.5 Å2 / Biso mean: 25.146 Å2 / Biso min: 9.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→29.488 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1688 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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