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Yorodumi- PDB-3gbj: Crystal structure of the motor domain of kinesin KIF13B bound with ADP -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gbj | ||||||
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Title | Crystal structure of the motor domain of kinesin KIF13B bound with ADP | ||||||
Components | KIF13B protein | ||||||
Keywords | MOTOR PROTEIN / kinesin / motor domain / ADP / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / ATP-binding / Microtubule / Nucleotide-binding | ||||||
Function / homology | Function and homology information plus-end-directed vesicle transport along microtubule / cytoskeleton-dependent intracellular transport / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / regulation of axonogenesis / microtubule-based movement / protein targeting / 14-3-3 protein binding ...plus-end-directed vesicle transport along microtubule / cytoskeleton-dependent intracellular transport / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / regulation of axonogenesis / microtubule-based movement / protein targeting / 14-3-3 protein binding / T cell activation / microtubule binding / microtubule / axon / protein kinase binding / signal transduction / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.102 Å | ||||||
Authors | Tong, Y. / Shen, L. / Shen, Y. / Tempel, W. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the motor domain of kinesin KIF13B bound with ADP Authors: Tong, Y. / Shen, L. / Shen, Y. / Tempel, W. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gbj.cif.gz | 348.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gbj.ent.gz | 278 KB | Display | PDB format |
PDBx/mmJSON format | 3gbj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gbj_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 3gbj_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 3gbj_validation.xml.gz | 33 KB | Display | |
Data in CIF | 3gbj_validation.cif.gz | 45.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/3gbj ftp://data.pdbj.org/pub/pdb/validation_reports/gb/3gbj | HTTPS FTP |
-Related structure data
Related structure data | 1i6iS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN AT THE TIME OF DEPOSITION |
-Components
#1: Protein | Mass: 39109.121 Da / Num. of mol.: 3 / Fragment: UNP residues 4-351 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIF13B / Plasmid: pET28a-LIC-CHis / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-V2R pRARE2 / References: UniProt: A0JLQ2, UniProt: Q9NQT8*PLUS #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-UNX / #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: 2.49 Å3/Da / Density % sol: 50.56 % Description: The structure factor file contains Friedel pairs |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 18% PEG 3350, Ammonium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→40 Å / Num. obs: 133690 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.065 / Χ2: 1.356 / Net I/σ(I): 10.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1I6I Resolution: 2.102→39.062 Å / FOM work R set: 0.797 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The Friedel pairs were used in phasing. Programs coot, molprobity have also been used in refinement
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Solvent computation | Shrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.55 Å2 / ksol: 0.337 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 162.21 Å2 / Biso mean: 46.3 Å2 / Biso min: 15.75 Å2
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Refinement step | Cycle: LAST / Resolution: 2.102→39.062 Å
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Refinement TLS params. | S33: -0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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