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Yorodumi- PDB-4qmh: The XMAP215 family drives microtubule polymerization using a stru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qmh | ||||||
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Title | The XMAP215 family drives microtubule polymerization using a structurally diverse TOG array | ||||||
Components | LP04448p | ||||||
Keywords | PROTEIN BINDING / TOG DOMAIN | ||||||
Function / homology | Function and homology information establishment or maintenance of neuroblast polarity / bicoid mRNA localization / microtubule plus end polymerase / pronuclear fusion / oocyte microtubule cytoskeleton organization / establishment or maintenance of microtubule cytoskeleton polarity / mitotic spindle elongation / microtubule plus-end / female meiotic nuclear division / positive regulation of microtubule nucleation ...establishment or maintenance of neuroblast polarity / bicoid mRNA localization / microtubule plus end polymerase / pronuclear fusion / oocyte microtubule cytoskeleton organization / establishment or maintenance of microtubule cytoskeleton polarity / mitotic spindle elongation / microtubule plus-end / female meiotic nuclear division / positive regulation of microtubule nucleation / microtubule plus-end binding / endoplasmic reticulum organization / oogenesis / microtubule polymerization / establishment of mitotic spindle orientation / centrosome duplication / cytoplasmic microtubule organization / tubulin binding / mitotic spindle organization / axon guidance / spindle / kinetochore / spindle pole / mitotic cell cycle / microtubule binding / centrosome / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.652 Å | ||||||
Authors | Fox, J.C. / Howard, A.E. / Currie, J.D. / Rogers, S.L. / Slep, K.C. | ||||||
Citation | Journal: Mol.Biol.Cell / Year: 2014 Title: The XMAP215 family drives microtubule polymerization using a structurally diverse TOG array. Authors: Fox, J.C. / Howard, A.E. / Currie, J.D. / Rogers, S.L. / Slep, K.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qmh.cif.gz | 110 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qmh.ent.gz | 83.5 KB | Display | PDB format |
PDBx/mmJSON format | 4qmh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/4qmh ftp://data.pdbj.org/pub/pdb/validation_reports/qm/4qmh | HTTPS FTP |
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-Related 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: 26303.529 Da / Num. of mol.: 1 / Fragment: TOG domain 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG5000, CG5000 Dmel_CG5000, Dmel_CG5000, msps / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 De3 Plyss / References: UniProt: Q9VEZ3 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.85 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 15 mg/ml protein concentration, 21% PEG 4000, 100 mM Tris pH 8.5, and 400 mM Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.12714, 0.97957 | |||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 8, 2007 | |||||||||
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.65→70 Å / Num. all: 45402 / Num. obs: 25054 / % possible obs: 95.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Biso Wilson estimate: 18.2 Å2 / Rsym value: 0.021 / Net I/σ(I): 33 | |||||||||
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 5.7 / Num. unique all: 2355 / Rsym value: 0.117 / % possible all: 88.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.652→29.907 Å / SU ML: 0.18 / σ(F): 0.05 / Phase error: 18.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.103 Å2 / ksol: 0.372 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.652→29.907 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 24.1554 Å / Origin y: 10.4333 Å / Origin z: 10.0088 Å
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Refinement TLS group | Selection details: all |