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- PDB-3gwr: Crystal structure of Putative calcium/calmodulin-dependent protei... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gwr | ||||||
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Title | Crystal structure of Putative calcium/calmodulin-dependent protein kinase type II association domain (YP_315894.1) from THIOBACILLUS DENITRIFICANS ATCC 25259 at 2.00 A resolution | ||||||
![]() | Putative calcium/calmodulin-dependent protein kinase type II association domain | ||||||
![]() | PROTEIN BINDING / YP_315894.1 / Putative calcium/calmodulin-dependent protein kinase type II association domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / TRANSFERASE | ||||||
Function / homology | SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Unknown ligand / SnoaL-like domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of Putative calcium/calmodulin-dependent protein kinase type II association domain (YP_315894.1) from THIOBACILLUS DENITRIFICANS ATCC 25259 at 2.00 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.5 KB | Display | ![]() |
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PDB format | ![]() | 51.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.8 KB | Display | ![]() |
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Full document | ![]() | 459.4 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 17.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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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 | CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
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Components
#1: Protein | Mass: 15965.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Tbd_2136, YP_315894.1 / Plasmid: SpeedET / Production host: ![]() ![]() #2: Chemical | Num. of mol.: 2 / Source method: obtained synthetically #3: Chemical | ChemComp-PG4 / #4: Water | ChemComp-HOH / | Sequence details | SEQUENCE THIS CONSTRUCT (WITH MUTATION E14D) WAS EXPRESSED WITH A PURIFICATION TAG ...SEQUENCE THIS CONSTRUCT (WITH MUTATION E14D) WAS EXPRESSED WITH A PURIFICATI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.16 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.2000M NH4F, 20.0000% PEG-3350, No Buffer pH 6.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 17, 2009 / Details: Flat collimating mirror, toroid focusing mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→28.892 Å / Num. obs: 22722 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.968 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 9.23 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() 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. PG4 MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. 5. AN UNKNOWN LIGAND (UNL) RESEMBLING BENZOIC ACID OR NITROBENZENE IS MODELED NEAR RESIDUE HIS 122 IN BOTH CHAINS. 6. LOOP REGION RESIDUES 94-98 ARE DISORDRED AND HAVE POOR DENSITY SUPPORT.
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.38 Å2 / Biso mean: 38.927 Å2 / Biso min: 20.99 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→28.892 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: 1547 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.005→2.058 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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