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Yorodumi- PDB-1mma: X-RAY STRUCTURES OF THE MGADP, MGATPGAMMAS, AND MGAMPPNP COMPLEXE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mma | ||||||
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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 / ADP / 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 / contractile actin filament bundle assembly / cell trailing edge ...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 / 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 / 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 / substrate-dependent cell migration, cell extension / myosin filament / filopodium assembly / early phagosome / myosin II complex / cortical actin cytoskeleton organization / microfilament motor activity / cortical actin cytoskeleton / pseudopodium / cytoskeletal motor activity / cleavage furrow / mitotic cytokinesis / response to mechanical stimulus / 14-3-3 protein binding / response to cAMP / extracellular matrix / cell motility / response to hydrogen peroxide / actin filament binding / chemotaxis / protein localization / regulation of cell shape / cell cortex / cytoplasmic vesicle / calmodulin binding / cytoskeleton / ATP binding / identical protein binding / cytosol 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mma.cif.gz | 167.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mma.ent.gz | 128.3 KB | Display | PDB format |
PDBx/mmJSON format | 1mma.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mma_validation.pdf.gz | 455.5 KB | Display | wwPDB validaton report |
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Full document | 1mma_full_validation.pdf.gz | 514.4 KB | Display | |
Data in XML | 1mma_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 1mma_validation.cif.gz | 36.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/1mma ftp://data.pdbj.org/pub/pdb/validation_reports/mm/1mma | HTTPS FTP |
-Related structure data
Related structure data | 1mmgC 1mmnC 1mmdS S: Starting model for refinement C: citing same article (ref.) |
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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: 86820.219 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+, ADP Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Production host: Dictyostelium discoideum (eukaryote) / References: UniProt: P08799, EC: 3.6.1.32 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ADP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.25 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 |
Detector | Date: Aug 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 56984 / % possible obs: 96.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.1→2.19 Å / % possible all: 90.5 |
Reflection | *PLUS Num. measured all: 189699 |
Reflection shell | *PLUS % possible obs: 90.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MMD Resolution: 2.1→20 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.219 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 47.3 Å2 | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.009 |