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- PDB-5fm8: Structure of the C-terminally extended domain My4 of human myomes... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fm8 | ||||||
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Title | Structure of the C-terminally extended domain My4 of human myomesin (space group P65) | ||||||
![]() | MYOMESIN-1 | ||||||
![]() | STRUCTURAL PROTEIN / SARCOMERE / M-BAND / FIBRONECTIN DOMAIN | ||||||
Function / homology | ![]() extraocular skeletal muscle development / striated muscle myosin thick filament / protein kinase A signaling / M band / structural constituent of muscle / sarcomere organization / positive regulation of protein secretion / kinase binding / positive regulation of gene expression / protein homodimerization activity / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pernigo, S. / Steiner, R.A. | ||||||
![]() | ![]() Title: Binding of Myomesin to Obscurin-Like-1 at the Muscle M-Band Provides a Strategy for Isoform-Specific Mechanical Protection. Authors: Pernigo, S. / Fukuzawa, A. / Beedle, A.E. / Holt, M. / Round, A. / Pandini, A. / Garcia-Manyes, S. / Gautel, M. / Steiner, R.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 | ![]() | 173.3 KB | Display | ![]() |
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PDB format | ![]() | 141.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5fm4C ![]() 5fm5SC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12186.966 Da / Num. of mol.: 4 Fragment: MY4 EXTENDED AT ITS C-TERMINUS, UNP RESIDUES 510-618 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-TRS / | #4: Water | ChemComp-HOH / | Sequence details | FIRST THREE N-TERMINAL RESIDUES ARE DERIVED FROM THE CLONING STRATEGY | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.18 % / Description: NONE |
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Crystal grow | pH: 8.8 Details: 21 % (W/V) PEG 2000 MME, 10 MM NICL2, 100 MM TRIS/HCL PH 8.8 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.05→84.36 Å / Num. obs: 35371 / % possible obs: 99.9 % / Observed criterion σ(I): -1 / Redundancy: 20 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.4 | |||||||||||||||
Reflection shell | Resolution: 2.05→2.11 Å / Redundancy: 20 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.6 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5FM5 Resolution: 2.05→84.36 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.655 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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 mean: 50.102 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→84.36 Å
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Refine LS restraints |
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