[English] 日本語
Yorodumi- PDB-5wj7: Crystal Structure of Amino Acids 1733-1797 of Human Beta Cardiac ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wj7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Amino Acids 1733-1797 of Human Beta Cardiac Myosin Fused to Xrcc4 | ||||||
Components | DNA repair protein XRCC4,Myosin-7 | ||||||
Keywords | Actin/DNA Binding Protein / Myosin / Xrcc4 / Coiled-Coil / Actin-DNA Binding Protein complex | ||||||
Function / homology | Function and homology information FHA domain binding / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / muscle myosin complex / muscle filament sliding / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination ...FHA domain binding / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / muscle myosin complex / muscle filament sliding / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / regulation of the force of heart contraction / protein localization to site of double-strand break / 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 / microfilament motor activity / ventricular cardiac muscle tissue morphogenesis / myofibril / cellular response to lithium ion / 2-LTR circle formation / skeletal muscle contraction / response to X-ray / striated muscle contraction / SUMOylation of DNA damage response and repair proteins / ATP metabolic process / stress fiber / cardiac muscle contraction / regulation of heart rate / sarcomere / muscle contraction / Nonhomologous End-Joining (NHEJ) / Z disc / double-strand break repair via nonhomologous end joining / double-strand break repair / actin filament binding / site of double-strand break / calmodulin binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 | 5wj7.cif.gz | 172.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5wj7.ent.gz | 135.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wj7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/5wj7 ftp://data.pdbj.org/pub/pdb/validation_reports/wj/5wj7 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5wjbC 5wlqC 5wlzC 5wmeC 1ik9S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22595.488 Da / Num. of mol.: 2 Fragment: UNP Q13426 residues 2-132, UNP P12883 residues 1733-1797 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC4, MYH7, MYHCB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): CodonPlus / References: UniProt: Q13426, UniProt: P12883 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.6 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 16% (w/v) Methyl-Ether PEG 5K, 300 mM glycine, 100 mM triethanolamine pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→100 Å / Num. obs: 21429 / % possible obs: 99.6 % / Redundancy: 12 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 53.6 |
Reflection shell | Resolution: 2.43→2.47 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 7.86 / Num. unique obs: 1036 / % possible all: 97.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IK9 Resolution: 2.5→39.243 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.26
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→39.243 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|