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Yorodumi- PDB-3i5i: The crystal structure of squid myosin S1 in the presence of SO4 2- -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i5i | |||||||||
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Title | The crystal structure of squid myosin S1 in the presence of SO4 2- | |||||||||
Components |
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Keywords | CONTRACTILE PROTEIN / SQUID / RIGOR-LIKE / NUCLEOTIDE FREE / MYOSIN S1 | |||||||||
Function / homology | Function and homology information cytoskeletal motor regulator activity / mitotic actomyosin contractile ring / mitotic actomyosin contractile ring contraction / muscle myosin complex / myosin filament / actomyosin structure organization / myosin II complex / locomotion / sarcomere organization / microfilament motor activity ...cytoskeletal motor regulator activity / mitotic actomyosin contractile ring / mitotic actomyosin contractile ring contraction / muscle myosin complex / myosin filament / actomyosin structure organization / myosin II complex / locomotion / sarcomere organization / microfilament motor activity / myofibril / myosin heavy chain binding / mitotic cytokinesis / muscle contraction / post-embryonic development / actin filament binding / calcium ion binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Loligo pealei (longfin inshore squid) Todarodes pacificus (Japanese flying squid) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | |||||||||
Authors | Yang, Y. / Gourinath, S. / Kovacs, M. / Nyitray, L. / Reutzel, R. / Himmel, D.M. / O'Neall-Hennessey, E. / Reshetnikova, L. / Szent-Gyorgyi, A.G. / Brown, J.H. / Cohen, C. | |||||||||
Citation | Journal: Structure / Year: 2007 Title: Rigor-like structures from muscle myosins reveal key mechanical elements in the transduction pathways of this allosteric motor. Authors: Yang, Y. / Gourinath, S. / Kovacs, M. / Nyitray, L. / Reutzel, R. / Himmel, D.M. / O'Neall-Hennessey, E. / Reshetnikova, L. / Szent-Gyorgyi, A.G. / Brown, J.H. / Cohen, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i5i.cif.gz | 213.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i5i.ent.gz | 171.5 KB | Display | PDB format |
PDBx/mmJSON format | 3i5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i5i_validation.pdf.gz | 471.1 KB | Display | wwPDB validaton report |
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Full document | 3i5i_full_validation.pdf.gz | 574.2 KB | Display | |
Data in XML | 3i5i_validation.xml.gz | 53.7 KB | Display | |
Data in CIF | 3i5i_validation.cif.gz | 71.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/3i5i ftp://data.pdbj.org/pub/pdb/validation_reports/i5/3i5i | HTTPS FTP |
-Related structure data
Related structure data | 2ec6C 2os8C 2otgC 3i5fC 3i5gC 3i5hC 2ovk C: citing same article (ref.) S: Starting model for refinement |
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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: 95939.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Loligo pealei (longfin inshore squid) / References: UniProt: O44934 |
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#2: Protein | Mass: 17577.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Todarodes pacificus (Japanese flying squid) References: UniProt: P08052 |
#3: Protein | Mass: 18081.236 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Todarodes pacificus (Japanese flying squid) References: UniProt: P05945 |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-CA / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.15 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 8% PEG 5000 MME, 150MM NACL, 100MM HEPES, 5% ETHYLENE GLYCOL, 5MM MGAC2, 2MM CAAC2, 2MM NAN3, 2MM BETA-MERCAPTOETHANOL, 20MM (NH4)2SO4, PH 7.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 |
Detector | Date: Nov 5, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. all: 22054 / Num. obs: 21926 / % possible obs: 97.1 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 16.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2OVK 2ovk Resolution: 3.3→50 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 3.3→50 Å
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Refine LS restraints |
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