+Open data
-Basic information
Entry | Database: PDB / ID: 4aki | ||||||
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Title | Dynein Motor Domain - LuAc derivative | ||||||
Components | GLUTATHIONE S-TRANSFERASE CLASS-MU 26 KDA ISOZYME, DYNEIN HEAVY CHAIN CYTOPLASMIC | ||||||
Keywords | MOTOR PROTEIN / DYNEIN / DYNEIN HEAVY CHAIN / DYNEIN MOTOR DOMAIN / MOTOR PROTEIN AAA+ PROTEIN / ASCE PROTEIN / P-LOOP NTPASE / CYTOSKELETAL MOTOR | ||||||
Function / homology | Function and homology information karyogamy / establishment of mitotic spindle localization / astral microtubule / nuclear migration along microtubule / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / spindle pole body / nuclear migration / dynein intermediate chain binding ...karyogamy / establishment of mitotic spindle localization / astral microtubule / nuclear migration along microtubule / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / spindle pole body / nuclear migration / dynein intermediate chain binding / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / glutathione transferase / glutathione transferase activity / cytoplasmic microtubule / cytoplasmic microtubule organization / Neutrophil degranulation / mitotic spindle organization / cell cortex / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | SCHISTOSOMA JAPONICUM (invertebrata) SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.7 Å | ||||||
Authors | Schmidt, H. / Gleave, E.S. / Carter, A.P. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2012 Title: Insights Into Dynein Motor Domain Function from a 3.3 Angstrom Crystal Structure Authors: Schmidt, H. / Gleave, E.S. / Carter, A.P. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aki.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4aki.ent.gz | 849.8 KB | Display | PDB format |
PDBx/mmJSON format | 4aki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/4aki ftp://data.pdbj.org/pub/pdb/validation_reports/ak/4aki | HTTPS FTP |
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-Related 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: 310205.125 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-218,1364-3038,3292-4092 Source method: isolated from a genetically manipulated source Details: CHIMERIC PROTEIN Source: (gene. exp.) SCHISTOSOMA JAPONICUM (invertebrata), (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) References: UniProt: P08515, UniProt: P36022, glutathione transferase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.75 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.34072 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 6, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34072 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→49.13 Å / Num. obs: 88918 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 3.7→3.77 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 3.7→49.14 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.913 / SU B: 41.941 / SU ML: 0.626 / Cross valid method: THROUGHOUT / ESU R Free: 0.764 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 192.237 Å2
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Refinement step | Cycle: LAST / Resolution: 3.7→49.14 Å
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