+Open data
-Basic information
Entry | Database: PDB / ID: 2ncd | ||||||
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Title | NCD (NON-CLARET DISJUNCTIONAL) DIMER FROM D. MELANOGASTER | ||||||
Components | PROTEIN (Kinesin motor NCD) | ||||||
Keywords | CONTRACTILE PROTEIN / KINESIN / MICROTUBULE-BASED MOTOR / NCD | ||||||
Function / homology | Function and homology information minus-end directed microtubule sliding / distributive segregation / regulation of mitotic spindle elongation / meiotic spindle assembly / mitotic spindle elongation / mitotic spindle microtubule / meiotic spindle organization / spindle assembly involved in female meiosis / minus-end-directed microtubule motor activity / regulation of mitotic spindle assembly ...minus-end directed microtubule sliding / distributive segregation / regulation of mitotic spindle elongation / meiotic spindle assembly / mitotic spindle elongation / mitotic spindle microtubule / meiotic spindle organization / spindle assembly involved in female meiosis / minus-end-directed microtubule motor activity / regulation of mitotic spindle assembly / microtubule bundle formation / meiotic spindle / mitotic centrosome separation / spindle organization / mitotic spindle assembly / mRNA transport / mitotic spindle organization / chromosome segregation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / spindle / microtubule binding / hydrolase activity / cell division / centrosome / protein homodimerization activity / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Sablin, E.P. / Case, R.B. / Dai, S.C. / Hart, C.L. / Ruby, A. / Vale, R.D. / Fletterick, R.J. | ||||||
Citation | Journal: Nature / Year: 1998 Title: Direction determination in the minus-end-directed kinesin motor ncd. Authors: Sablin, E.P. / Case, R.B. / Dai, S.C. / Hart, C.L. / Ruby, A. / Vale, R.D. / Fletterick, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ncd.cif.gz | 86.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ncd.ent.gz | 64.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ncd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/2ncd ftp://data.pdbj.org/pub/pdb/validation_reports/nc/2ncd | 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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Unit cell |
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-Components
#1: Protein | Mass: 47735.836 Da / Num. of mol.: 1 / Fragment: RESIDUES 281-700 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Description: BACTERIAL EXPRESSION / Gene: NCD / Plasmid: PHB40P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSE / References: UniProt: P20480 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ADP / | #4: 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: 2.8 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: THE MOTHER LIQUOR CONTAINED PROTEIN AT ABOUT 20 MG/ML, 2 MM ADP, 10 MM MGCL2, 100 MM NACL, 700 MM LI2SO4, 1 MM EGTA, AND 1 MM DTT IN 20 MM HEPES, PH 7.5. THE RESERVOIR WAS 1.4 M LI2SO4, 10 ...Details: THE MOTHER LIQUOR CONTAINED PROTEIN AT ABOUT 20 MG/ML, 2 MM ADP, 10 MM MGCL2, 100 MM NACL, 700 MM LI2SO4, 1 MM EGTA, AND 1 MM DTT IN 20 MM HEPES, PH 7.5. THE RESERVOIR WAS 1.4 M LI2SO4, 10 MM MGCL2, 1 MM EGTA, 1 MM DTT IN 20 MM HEPES, PH 7.5., VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Detector: IMAGE PLATE / Date: Oct 15, 1997 |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. all: 18795 / Num. obs: 18795 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.3→2.5 Å / Redundancy: 5 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 5 / Rsym value: 0.13 / % possible all: 92.6 |
Reflection | *PLUS Num. measured all: 190358 |
Reflection shell | *PLUS % possible obs: 92.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NCD MONOMER Resolution: 2.5→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 23.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.6 Å / Total num. of bins used: 5
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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