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Yorodumi- PDB-4a5y: Intermediate state of human kinesin Eg5 in complex with Ispinesib -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a5y | ||||||
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Title | Intermediate state of human kinesin Eg5 in complex with Ispinesib | ||||||
Components | KINESIN-LIKE PROTEIN KIF11 | ||||||
Keywords | MOTOR PROTEIN / MITOSIS | ||||||
Function / homology | Function and homology information spindle elongation / Kinesins / plus-end-directed microtubule motor activity / regulation of mitotic centrosome separation / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / spindle organization / microtubule-based movement ...spindle elongation / Kinesins / plus-end-directed microtubule motor activity / regulation of mitotic centrosome separation / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / spindle organization / microtubule-based movement / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / mitotic spindle / spindle / spindle pole / mitotic cell cycle / microtubule binding / microtubule / cell division / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Kaan, H.Y.K. / Kozielski, F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: "Snapshots" of Ispinesib-Induced Conformational Changes in the Mitotic Kinesin Eg5. Authors: Kaan, H.Y.K. / Major, J. / Tkocz, K. / Kozielski, F. / Rosenfeld, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a5y.cif.gz | 214.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a5y.ent.gz | 170.3 KB | Display | PDB format |
PDBx/mmJSON format | 4a5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/4a5y ftp://data.pdbj.org/pub/pdb/validation_reports/a5/4a5y | HTTPS FTP |
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-Related structure data
Related structure data | 1x88S 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
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 41055.582 Da / Num. of mol.: 3 / Fragment: MOTOR DOMAIN, RESIDUES 1-368 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P52732 |
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-Non-polymers , 6 types, 353 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MG / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.13 % / Description: NONE |
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Crystal grow | pH: 6.8 Details: 14 % POLYETHYLENE GLYCOL-3350, 0.18 M AMMONIUM PHOSPHATE, pH 6.8 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→30 Å / Num. obs: 48178 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Biso Wilson estimate: 44.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2.45→2.58 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.4 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1X88 Resolution: 2.45→29.603 Å / SU ML: 0.68 / σ(F): 1.34 / Phase error: 27.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.652 Å2 / ksol: 0.331 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→29.603 Å
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Refine LS restraints |
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LS refinement shell |
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