[English] 日本語
![](img/lk-miru.gif)
- PDB-1w9j: Myosin II Dictyostelium discoideum motor domain S456Y bound with ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1w9j | ||||||
---|---|---|---|---|---|---|---|
Title | Myosin II Dictyostelium discoideum motor domain S456Y bound with MgADP-AlF4 | ||||||
![]() | MYOSIN II HEAVY CHAIN | ||||||
![]() | MYOSIN / MOLECULAR MOTOR / ATPASE / MOTOR DOMAIN / MUTANT / MUSCLE CONTRACTION | ||||||
Function / homology | ![]() calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / equatorial cell cortex / contractile actin filament bundle assembly / cell trailing edge / contractile vacuole organization ...calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / equatorial cell cortex / contractile actin filament bundle assembly / cell trailing edge / contractile vacuole organization / myosin filament assembly / aggregation involved in sorocarp development / culmination involved in sorocarp development / RHO GTPases activate PAKs / adenyl nucleotide binding / response to differentiation-inducing factor 1 / hypotonic response / uropod / mitotic actomyosin contractile ring / actomyosin contractile ring / mitotic actomyosin contractile ring contraction / actin-myosin filament sliding / detection of mechanical stimulus / apical cortex / negative regulation of actin filament polymerization / bleb assembly / actomyosin / substrate-dependent cell migration, cell extension / myosin filament / filopodium assembly / early phagosome / cortical actin cytoskeleton organization / myosin II complex / cortical actin cytoskeleton / microfilament motor activity / pseudopodium / cytoskeletal motor activity / cleavage furrow / mitotic cytokinesis / response to mechanical stimulus / 14-3-3 protein binding / response to cAMP / extracellular matrix / muscle contraction / cell motility / response to hydrogen peroxide / protein localization / chemotaxis / actin filament binding / cell cortex / regulation of cell shape / cytoplasmic vesicle / cytoskeleton / calmodulin binding / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Morris, C.A. / Coureux, P.-D. / Wells, A.L. / Houdusse, A. / Sweeney, H.L. | ||||||
![]() | ![]() Title: Structure-Function Analysis of Myosin II Backdoor Mutants Authors: Morris, C.A. / Coureux, P.-D. / Wells, A.L. / Houdusse, A. / Sweeney, H.L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 168.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 129.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 787.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 793.3 KB | Display | |
Data in XML | ![]() | 30.4 KB | Display | |
Data in CIF | ![]() | 45.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1w9iC ![]() 1w9kC ![]() 1w9lC ![]() 1mndS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 87897.344 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, RESIDUES 1-755 / Mutation: YES Source method: isolated from a genetically manipulated source Details: MGADP-BEFX / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 397 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/ALF.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/ALF.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / | ||
---|---|---|---|
#3: Chemical | ChemComp-ADP / | ||
#4: Chemical | ChemComp-ALF / | ||
#5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
-Details
Compound details | ENGINEERED RESIDUE ASP 2 ASN, CHAIN A ENGINEERED RESIDUE SER 456 TYR, CHAIN A MYOSIN IS A PROTEIN ...ENGINEERED |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 59.4 % |
---|---|
Crystal grow | pH: 7 Details: 12% PEG 8000, 50 MM HEPES PH 7, 100 MM NACL, 2 MM DTT, 2 MM NAN3 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 24, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2→76.7 Å / Num. obs: 63165 / % possible obs: 89.4 % / Observed criterion σ(I): 3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.98→2.03 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2.9 / % possible all: 44.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1MND Resolution: 2→76.7 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.04 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.25 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→76.7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|