+Open data
-Basic information
Entry | Database: PDB / ID: 7klj | ||||||
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Title | Crystal structure of the WD-repeat domain of human KIF21A | ||||||
Components | Isoform 2 of Kinesin-like protein KIF21A | ||||||
Keywords | MOTOR PROTEIN / KIF21A / WD-repeat / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information ankyrin repeat binding / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / microtubule-based movement / microtubule binding / microtubule / axon / dendrite ...ankyrin repeat binding / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / microtubule-based movement / microtubule binding / microtubule / axon / dendrite / ATP hydrolysis activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | ||||||
Authors | Zeng, H. / Dong, A. / Loppnau, P. / Hutchinson, A. / Seitova, A. / Edwards, A.M. / Arrowsmith, C.H. / Halabelian, L. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the WD-repeat domain of human KIF21A Authors: Zeng, H. / Dong, A. / Loppnau, P. / Hutchinson, A. / Seitova, A. / Edwards, A.M. / Arrowsmith, C.H. / Halabelian, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7klj.cif.gz | 148.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7klj.ent.gz | 115.1 KB | Display | PDB format |
PDBx/mmJSON format | 7klj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/7klj ftp://data.pdbj.org/pub/pdb/validation_reports/kl/7klj | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36751.621 Da / Num. of mol.: 2 / Fragment: WD repeat (UNP residues 1324-1640) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIF21A, KIAA1708, KIF2 / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q7Z4S6 #2: Chemical | #3: Chemical | ChemComp-UNX / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.01 Å3/Da / Density % sol: 38.76 % / Mosaicity: 0.482 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 25% PEG3350, 0.2 M ammonium acetate, 0.1 M HEPES, pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Sep 20, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.52→50 Å / Num. obs: 89050 / % possible obs: 99.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.029 / Rrim(I) all: 0.078 / Χ2: 1.454 / Net I/σ(I): 12.2 / Num. measured all: 600649 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→20.2 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.167 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.071 / 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 max: 58.47 Å2 / Biso mean: 18.778 Å2 / Biso min: 11.45 Å2
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Refinement step | Cycle: final / Resolution: 1.52→20.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.52→1.558 Å / Rfactor Rfree error: 0
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