[English] 日本語
Yorodumi- PDB-1s5g: Structure of Scallop myosin S1 reveals a novel nucleotide conformation -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s5g | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Scallop myosin S1 reveals a novel nucleotide conformation | ||||||
Components |
| ||||||
Keywords | CONTRACTILE PROTEIN / Scallop myosin S1 / Near Rigor / complex salt bridge / novel conformation of nucleotide | ||||||
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 / calmodulin binding / calcium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Argopecten irradians (bay scallop) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Risal, D. / Gourinath, S. / Himmel, D.M. / Szent-Gyorgyi, A.G. / Cohen, C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2004 Title: Myosin subfragment 1 structures reveal a partially bound nucleotide and a complex salt bridge that helps couple nucleotide and actin binding. Authors: Risal, D. / Gourinath, S. / Himmel, D.M. / Szent-Gyorgyi, A.G. / Cohen, C. #1: Journal: Structure / Year: 2003 Title: Crystal Structure Of Scallop Myosin S1 In The Pre-Power Stroke State To 2.6 A Resolution: Flexibility and Function In The Head Authors: Gourinath, S. / Himmel, D.M. / Brown, J.H. / Reshetnikova, L. / Szent-Gyorgyi, A.G. / Cohen, C. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: Crystallographic findings on the internally uncoupled and near-rigor states of myosin: further insights into the mechanics of the motor Authors: Himmel, D.M. / Gourinath, S. / Reshetnikova, L. / Shen, Y. / Szent-Gyorgyi, A.G. / Cohen, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1s5g.cif.gz | 231.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1s5g.ent.gz | 181 KB | Display | PDB format |
PDBx/mmJSON format | 1s5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1s5g_validation.pdf.gz | 856.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1s5g_full_validation.pdf.gz | 912.3 KB | Display | |
Data in XML | 1s5g_validation.xml.gz | 45.2 KB | Display | |
Data in CIF | 1s5g_validation.cif.gz | 61 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s5/1s5g ftp://data.pdbj.org/pub/pdb/validation_reports/s5/1s5g | HTTPS FTP |
-Related structure data
Related structure data | 1sr6C 1kk7S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 3 types, 3 molecules AYZ
#1: Protein | Mass: 95815.062 Da / Num. of mol.: 1 / Fragment: Residues 1-840 / Source method: isolated from a natural source / Source: (natural) Argopecten irradians (bay scallop) / References: UniProt: P24733 |
---|---|
#2: Protein | Mass: 17560.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Argopecten irradians (bay scallop) / References: UniProt: P13543 |
#3: Protein | Mass: 17635.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Argopecten irradians (bay scallop) / References: UniProt: P07291 |
-Non-polymers , 5 types, 5 molecules
#4: Chemical | ChemComp-SO4 / |
---|---|
#5: Chemical | ChemComp-ADP / |
#6: Chemical | ChemComp-MG / |
#7: Chemical | ChemComp-CA / |
#8: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
---|
-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.9 % |
---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 8000, magnesium chloride, ADP, Glycerol, MES, TMAO, cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 24, 2002 |
Radiation | Monochromator: RH-COATED WITH SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. all: 22278 / Num. obs: 21309 / % possible obs: 85.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 80.5 Å2 / Rsym value: 0.071 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 1553 / Rsym value: 0.284 / % possible all: 59.1 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1kk7 Resolution: 3.1→43.44 Å / Isotropic thermal model: OVERALL ANISOTROPIC B VALUE / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.4 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→43.44 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|