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Yorodumi- PDB-5fm8: Structure of the C-terminally extended domain My4 of human myomes... -
+Open data
-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) | ||||||
Components | MYOMESIN-1 | ||||||
Keywords | STRUCTURAL PROTEIN / SARCOMERE / M-BAND / FIBRONECTIN DOMAIN | ||||||
Function / homology | Function and homology information extraocular skeletal muscle development / striated muscle myosin thick filament / M band / structural constituent of muscle / sarcomere organization / protein kinase A signaling / positive regulation of protein secretion / kinase binding / positive regulation of gene expression / protein homodimerization activity / identical protein binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Pernigo, S. / Steiner, R.A. | ||||||
Citation | Journal: Structure / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fm8.cif.gz | 173.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fm8.ent.gz | 141.4 KB | Display | PDB format |
PDBx/mmJSON format | 5fm8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/5fm8 ftp://data.pdbj.org/pub/pdb/validation_reports/fm/5fm8 | HTTPS FTP |
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-Related structure data
Related structure data | 5fm4C 5fm5SC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P52179 #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 | |||||||||||||||
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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