+Open data
-Basic information
Entry | Database: PDB / ID: 5fm5 | ||||||
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Title | Crystal structure of the myomesin:obscurin-like-1 complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / SARCOMERE / M-BAND / CYTOSKELETAL PROTEIN / PROTEIN COMPLEX / IMMUNOGLOBULIN-LIKE DOMAIN / FIBRONECTIN DOMAIN | ||||||
Function / homology | Function and homology information 3M complex / extraocular skeletal muscle development / striated muscle myosin thick filament / protein localization to Golgi apparatus / cardiac myofibril assembly / cytoskeletal anchor activity / M band / positive regulation of dendrite morphogenesis / structural constituent of muscle / regulation of mitotic nuclear division ...3M complex / extraocular skeletal muscle development / striated muscle myosin thick filament / protein localization to Golgi apparatus / cardiac myofibril assembly / cytoskeletal anchor activity / M band / positive regulation of dendrite morphogenesis / structural constituent of muscle / regulation of mitotic nuclear division / sarcomere organization / Golgi organization / intercalated disc / cytoskeleton organization / protein kinase A signaling / positive regulation of protein secretion / kinase binding / Z disc / microtubule cytoskeleton organization / Neddylation / centrosome / positive regulation of gene expression / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 | 5fm5.cif.gz | 196.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fm5.ent.gz | 160.3 KB | Display | PDB format |
PDBx/mmJSON format | 5fm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fm5_validation.pdf.gz | 449.6 KB | Display | wwPDB validaton report |
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Full document | 5fm5_full_validation.pdf.gz | 452.5 KB | Display | |
Data in XML | 5fm5_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 5fm5_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/5fm5 ftp://data.pdbj.org/pub/pdb/validation_reports/fm/5fm5 | HTTPS FTP |
-Related structure data
Related structure data | 5fm4C 5fm8C 2nziS 2wp3S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25292.723 Da / Num. of mol.: 2 / Fragment: MY4-MY5, RESIDUES 510-739 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P52179 #2: Protein | Mass: 11218.062 Da / Num. of mol.: 2 / Fragment: OL3 (THIRD IG DOMAIN), RESIDUES 251-339 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O75147 #3: Water | ChemComp-HOH / | Sequence details | N-TERMINAL M COMES FROM THE EXPRESSION | |
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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: 2.87 Å3/Da / Density % sol: 57.2 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 20% PEG8000, 0.2M MGCL2, 0.1M TRIS-HCL, PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9778 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 30, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→67.19 Å / Num. obs: 14811 / % possible obs: 99.1 % / Observed criterion σ(I): -1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 3.1→3.18 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.8 / % possible all: 98.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2NZI,2WP3 Resolution: 3.1→75.4 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.886 / SU B: 42.922 / SU ML: 0.354 / Cross valid method: THROUGHOUT / ESU R Free: 0.413 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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: 85.542 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→75.4 Å
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Refine LS restraints |
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