[English] 日本語
Yorodumi- PDB-5wme: Crystal Structure of Amino Acids 1729-1786 of Human Beta Cardiac ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wme | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Amino Acids 1729-1786 of Human Beta Cardiac Myosin Fused to Gp7 as Anti-Parallel Four-Helix Bundle | ||||||
Components | Capsid assembly scaffolding protein,Myosin-7 | ||||||
Keywords | MOTOR PROTEIN / Myosin / Gp7 / Coiled-Coil | ||||||
Function / homology | Function and homology information viral scaffold / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / muscle myosin complex / muscle filament sliding / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / myosin II complex / adult heart development ...viral scaffold / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / muscle myosin complex / muscle filament sliding / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / myosin II complex / adult heart development / cardiac muscle hypertrophy in response to stress / myosin complex / sarcomere organization / virion assembly / microfilament motor activity / ventricular cardiac muscle tissue morphogenesis / myofibril / skeletal muscle contraction / striated muscle contraction / stress fiber / ATP metabolic process / cardiac muscle contraction / regulation of heart rate / sarcomere / muscle contraction / Z disc / actin filament binding / calmodulin binding / DNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus phage phi29 (virus) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Andreas, M.P. / Ajay, G. / Gellings, J. / Rayment, I. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: J. Struct. Biol. / Year: 2017 Title: Design considerations in coiled-coil fusion constructs for the structural determination of a problematic region of the human cardiac myosin rod. Authors: Andreas, M.P. / Ajay, G. / Gellings, J.A. / Rayment, I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5wme.cif.gz | 159.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5wme.ent.gz | 126.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wme.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/5wme ftp://data.pdbj.org/pub/pdb/validation_reports/wm/5wme | HTTPS FTP |
---|
-Related structure data
Related structure data | 5wj7C 5wjbC 5wlqC 5wlzC 1no4S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 12354.793 Da / Num. of mol.: 4 Fragment: UNP P13848 residues 2-48, UNP P12883 residues 1729-1786 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage phi29 (virus), (gene. exp.) Homo sapiens (human) Gene: MYH7, MYHCB / Production host: Escherichia coli (E. coli) / References: UniProt: P13848, UniProt: P12883 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 39.5 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 18% (w/v) pentaerythritol ethoxylate 797, 150 mM ammonium thiocyanate, 100 mM sodium acetate pH 5.0. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 17830 / % possible obs: 99.4 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 868 / % possible all: 97 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NO4 Resolution: 2.3→44.867 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.88
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→44.867 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|