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- PDB-1prw: Crystal structure of bovine brain Ca++ calmodulin in a compact form -
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Open data
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Basic information
Entry | Database: PDB / ID: 1prw | ||||||
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Title | Crystal structure of bovine brain Ca++ calmodulin in a compact form | ||||||
![]() | Calmodulin | ||||||
![]() | METAL BINDING PROTEIN / EF HAND / CALCIUM-BINDING PROTEIN / KINASE ACTIVATOR | ||||||
Function / homology | ![]() positive regulation of ryanodine-sensitive calcium-release channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / spindle pole / protein domain specific binding / calcium ion binding / protein-containing complex / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Fallon, J.L. / Quiocho, F.A. | ||||||
![]() | ![]() Title: A closed compact structure of native ca(2+)-calmodulin. Authors: Fallon, J.L. / Quiocho, F.A. #2: ![]() Title: X-ray analysis reveals conformational adaptation of the linker in functional calmodulin mutants Authors: Meador, W.E. / George, S.E. / Means, A.R. / Quiocho, F.A. #3: ![]() Title: Modulation of calmodulin plasticity in molecular recognition on the basis of x-ray structures Authors: Meador, W.E. / Means, A.R. / Quiocho, F.A. #4: ![]() Title: Target enzyme recognition by calmodulin: 2.4 A structure of a calmodulin-peptide complex Authors: Meador, W.E. / Means, A.R. / Quiocho, F.A. #5: ![]() Title: Calmodulin structure refined at 1.7 A resolution Authors: Chattopadhyaya, R. / Meador, W.E. / Means, A.R. / Quiocho, F.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 43.4 KB | Display | ![]() |
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PDB format | ![]() | 33.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.6 KB | Display | ![]() |
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Full document | ![]() | 423.3 KB | Display | |
Data in XML | ![]() | 9.9 KB | Display | |
Data in CIF | ![]() | 13.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16789.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||
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#2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.69 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: PEG 6000, sodium acetate, glycerol, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / pH: 5.6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→14 Å / Num. all: 15132 / Num. obs: 13383 / % possible obs: 88.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.96 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.28 / Num. unique all: 1377 / Rsym value: 0.42 / % possible all: 90.7 |
Reflection | *PLUS Num. obs: 12598 / % possible obs: 92.4 % / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 90.7 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 4.8 |
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Processing
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Refinement | Method to determine structure: SIRSAS / Resolution: 1.7→14.59 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 533665.65 / Data cutoff high rms absF: 533665.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 1 / Stereochemistry target values: Engh & Huber Details: The atoms CE, NZ of Lys13 and CD, CE, NZ of Lys21 are present in the file even though the electron density for these atoms is missing
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 83.7254 Å2 / ksol: 0.462227 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→14.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.7 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.188 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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