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Yorodumi- PDB-2fme: Crystal structure of the mitotic kinesin eg5 (ksp) in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fme | ||||||
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Title | Crystal structure of the mitotic kinesin eg5 (ksp) in complex with mg-adp and (r)-4-(3-hydroxyphenyl)-n,n,7,8-tetramethyl-3,4-dihydroisoquinoline-2(1h)-carboxamide | ||||||
Components | Kinesin-like protein KIF11 | ||||||
Keywords | CELL CYCLE / Eg5 KSP Mg-ADP Complex Inhibitor | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Sheriff, S. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2006 Title: Inhibitors of human mitotic kinesin Eg5: Characterization of the 4-phenyl-tetrahydroisoquinoline lead series Authors: Tarby, C.M. / Kaltenbach III, R.F. / Huynh, T. / Pudzianowski, A. / Shen, H. / Ortega-Nanos, M. / Sheriff, S. / Newitt, J.A. / McDonnell, P.A. / Burford, N. / Fairchild, C.R. / Vaccaro, W. / ...Authors: Tarby, C.M. / Kaltenbach III, R.F. / Huynh, T. / Pudzianowski, A. / Shen, H. / Ortega-Nanos, M. / Sheriff, S. / Newitt, J.A. / McDonnell, P.A. / Burford, N. / Fairchild, C.R. / Vaccaro, W. / Chen, Z. / Borzilleri, R.M. / Naglich, J. / Lombardo, L.J. / Gottardis, M. / Trainor, G.L. / Roussell, D.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fme.cif.gz | 146.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fme.ent.gz | 112.9 KB | Display | PDB format |
PDBx/mmJSON format | 2fme.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/2fme ftp://data.pdbj.org/pub/pdb/validation_reports/fm/2fme | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 41055.582 Da / Num. of mol.: 2 / Fragment: Kinesin-motor domain (RESIDUES 1-368) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIF11, EG5, KNSL1 / Plasmid: pET28N / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P52732 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.68 Å3/Da / Density % sol: 54.02 % |
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Crystal grow | Temperature: 277 K / pH: 7.8 Details: 1:1 reservoir: 0.1 M NaHEPES pH 7.8, 0.2 M MgCl2, 23% PEG-3350; protein: 25 mg/ml (610 uM) in 25 mM PIPES pH 6.8, 200 mM NaCl, 2 mM DTT, 5 mM MgCl2, 1 mM EGTA, 2.5 mM ADP, 0.75% DMSO, uM (R)- ...Details: 1:1 reservoir: 0.1 M NaHEPES pH 7.8, 0.2 M MgCl2, 23% PEG-3350; protein: 25 mg/ml (610 uM) in 25 mM PIPES pH 6.8, 200 mM NaCl, 2 mM DTT, 5 mM MgCl2, 1 mM EGTA, 2.5 mM ADP, 0.75% DMSO, uM (R)-4-(3-HYDROXYPHENYL)-N,N,7,8-TETRAMETHYL-3,4-DIHYDROISOQUINOLINE-2(1H)-CARBOXAMIDE, vapor diffusion, hanging drop, temperature 277K, pH 7.80 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Mar 9, 2005 / Details: MICROMAX CONFOCAL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 47360 / % possible obs: 93.7 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 5.7 / % possible all: 71.7 |
-Phasing
Phasing MR | Rfactor: 43.8 / Cor.coef. Fo:Fc: 46.6 / Cor.coef. Io to Ic: 51.2
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Phasing dm | Method: Solvent flattening and Histogram matching / Reflection: 47350 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: INTERNAL MODEL OF EG5/LIGAND COMPLEX Resolution: 2.1→40 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2140759 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: Due to a feature in the refinement program, the structure was refined with an OXT on a residue that is not the terminal residue of the sequence. The OXT was changed to N of the next residue ...Details: Due to a feature in the refinement program, the structure was refined with an OXT on a residue that is not the terminal residue of the sequence. The OXT was changed to N of the next residue by the wwPDB annotation staff.
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Solvent computation | Solvent model: BABINET / Bsol: 280 Å2 / ksol: 0.9 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→40 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Rms dev Biso : 2 Å2 / Rms dev position: 0.036 Å / Weight Biso : 2 / Weight position: 300
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LS refinement shell | Resolution: 2.1→2.2 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 8
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Xplor file |
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