[English] 日本語
Yorodumi- PDB-1mmg: X-RAY STRUCTURES OF THE MGADP, MGATPGAMMAS, AND MGAMPPNP COMPLEXE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mmg | ||||||
---|---|---|---|---|---|---|---|
Title | X-RAY STRUCTURES OF THE MGADP, MGATPGAMMAS, AND MGAMPPNP COMPLEXES OF THE DICTYOSTELIUM DISCOIDEUM MYOSIN MOTOR DOMAIN | ||||||
Components | MYOSIN | ||||||
Keywords | COILED COIL / MYOSIN / DICTYOSTELIUM / MOTOR / NUCLEOTIDE ANALOGUES / ATPGS / ATPASE / ACTIN-BINDING | ||||||
Function / homology | Function and homology information calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / response to differentiation-inducing factor 1 / equatorial cell cortex / RHO GTPases activate PAKs / contractile actin filament bundle assembly ...calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / response to differentiation-inducing factor 1 / equatorial cell cortex / RHO GTPases activate PAKs / contractile actin filament bundle assembly / cell trailing edge / contractile vacuole organization / myosin filament assembly / aggregation involved in sorocarp development / culmination involved in sorocarp development / adenyl nucleotide binding / actomyosin contractile ring / hypotonic response / uropod / actin-myosin filament sliding / detection of mechanical stimulus / apical cortex / negative regulation of actin filament polymerization / bleb assembly / actomyosin / myosin filament / filopodium assembly / myosin II complex / early phagosome / microfilament motor activity / cortical actin cytoskeleton organization / cortical actin cytoskeleton / pseudopodium / cleavage furrow / cytoskeletal motor activity / mitotic cytokinesis / response to mechanical stimulus / response to cAMP / extracellular matrix / 14-3-3 protein binding / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Dictyostelium discoideum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Gulick, A.M. / Bauer, C.B. / Thoden, J.B. / Rayment, I. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: X-ray structures of the MgADP, MgATPgammaS, and MgAMPPNP complexes of the Dictyostelium discoideum myosin motor domain. Authors: Gulick, A.M. / Bauer, C.B. / Thoden, J.B. / Rayment, I. #1: Journal: Biochemistry / Year: 1995 Title: X-Ray Structures of the Myosin Motor Domain of Dictyostelium Discoideum Complexed with Mgadp(Dot)Befx and Mgadp(Dot)Alf4- Authors: Fisher, A.J. / Smith, C.A. / Thoden, J.B. / Smith, R. / Sutoh, K. / Holden, H.M. / Rayment, I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1mmg.cif.gz | 164.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1mmg.ent.gz | 129.5 KB | Display | PDB format |
PDBx/mmJSON format | 1mmg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/1mmg ftp://data.pdbj.org/pub/pdb/validation_reports/mm/1mmg | HTTPS FTP |
---|
-Related structure data
Related structure data | 1mmaC 1mmnC 1mmdS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 86781.086 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN / Mutation: Q760L, R761P, I762N Source method: isolated from a genetically manipulated source Details: GENETICALLY TRUNCATED HEAD OF MYOSIN FROM DICTYOSTELIUM. LIGANDS MG2+, ATPGS Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Production host: Dictyostelium discoideum (eukaryote) / References: UniProt: P08799, EC: 3.6.1.32 |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-AGS / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.65 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 113 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.908 |
Detector | Date: Jul 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 58467 / % possible obs: 97.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 91.6 |
Reflection | *PLUS Num. obs: 77182 / Num. measured all: 310844 |
Reflection shell | *PLUS % possible obs: 91.6 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MMD Resolution: 2.1→30 Å / σ(F): 0
| ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
| ||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||
Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.226 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 42.3 Å2 | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.007 |