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Yorodumi- PDB-3zfd: Crystal Structure of the Kif4 Motor Domain Complexed With Mg-AMPPNP -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zfd | ||||||
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Title | Crystal Structure of the Kif4 Motor Domain Complexed With Mg-AMPPNP | ||||||
Components | CHROMOSOME-ASSOCIATED KINESIN KIF4 | ||||||
Keywords | HYDROLASE / MOLECULAR MOTOR / ATPASE / MICROTUBULE | ||||||
Function / homology | Function and homology information Kinesins / mitotic spindle midzone assembly / Recycling pathway of L1 / spindle elongation / COPI-dependent Golgi-to-ER retrograde traffic / MHC class II antigen presentation / microtubule associated complex / microtubule motor activity / microtubule-based movement / iron-sulfur cluster binding ...Kinesins / mitotic spindle midzone assembly / Recycling pathway of L1 / spindle elongation / COPI-dependent Golgi-to-ER retrograde traffic / MHC class II antigen presentation / microtubule associated complex / microtubule motor activity / microtubule-based movement / iron-sulfur cluster binding / mitotic cytokinesis / mitotic spindle organization / chromosome / midbody / microtubule binding / microtubule / DNA binding / nucleoplasm / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Chang, Q. / Nitta, R. / Inoue, S. / Hirokawa, N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: Structural Basis for the ATP-Induced Isomerization of Kinesin. Authors: Chang, Q. / Nitta, R. / Inoue, S. / Hirokawa, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zfd.cif.gz | 85 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zfd.ent.gz | 60.9 KB | Display | PDB format |
PDBx/mmJSON format | 3zfd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/3zfd ftp://data.pdbj.org/pub/pdb/validation_reports/zf/3zfd | HTTPS FTP |
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-Related structure data
Related structure data | 3zfcC 3hqdS 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: 39068.371 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, RESIDUES 1-344 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: ICR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33174, EC: 3.6.4.4 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ANP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.72 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: pH 8.5 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→44.35 Å / Num. obs: 37057 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 11.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.1 |
Reflection shell | Highest resolution: 1.7 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.4 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3HQD Resolution: 1.71→44.35 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.706 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 15.211 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→44.35 Å
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Refine LS restraints |
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