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Yorodumi- PDB-5mvw: Complex between the Leucine Zipper (LZ) and Centrosomin-motif 2 (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mvw | |||||||||
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Title | Complex between the Leucine Zipper (LZ) and Centrosomin-motif 2 (CM2) domains of Drosophila melanogaster Centrosomin (Cnn) | |||||||||
Components | (CentrosominCDK5RAP2) x 2 | |||||||||
Keywords | CELL CYCLE / Centrosome / Centriole / Coiled-coil / Mitosis | |||||||||
Function / homology | Function and homology information photoreceptor cell morphogenesis / regulation of Golgi organization / pole cell formation / asymmetric cell division / regulation of centriole-centriole cohesion / asymmetric neuroblast division / positive regulation of microtubule nucleation / embryonic cleavage / peripheral nervous system development / motile cilium ...photoreceptor cell morphogenesis / regulation of Golgi organization / pole cell formation / asymmetric cell division / regulation of centriole-centriole cohesion / asymmetric neuroblast division / positive regulation of microtubule nucleation / embryonic cleavage / peripheral nervous system development / motile cilium / centrosome cycle / midgut development / pericentriolar material / centriole replication / centriole / mitotic spindle organization / ciliary basal body / meiotic cell cycle / central nervous system development / spindle pole / molecular adaptor activity / centrosome / Golgi apparatus Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | |||||||||
Authors | Feng, Z. / Johnson, S. / Raff, J.W. / Lea, S.M. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Cell / Year: 2017 Title: Structural Basis for Mitotic Centrosome Assembly in Flies. Authors: Feng, Z. / Caballe, A. / Wainman, A. / Johnson, S. / Haensele, A.F.M. / Cottee, M.A. / Conduit, P.T. / Lea, S.M. / Raff, J.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mvw.cif.gz | 102.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mvw.ent.gz | 83.4 KB | Display | PDB format |
PDBx/mmJSON format | 5mvw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mv/5mvw ftp://data.pdbj.org/pub/pdb/validation_reports/mv/5mvw | 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
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 8198.428 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Centrosomin CM2 domain residues 1082-1148 / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: cnn, Arr, CG4832 / Plasmid: pLip / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P54623 #2: Protein | Mass: 6550.455 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Centrosomin LZ domain residues 490-544 / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: cnn, Arr, CG4832 / Plasmid: pETM44 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): B834 / References: UniProt: P54623 |
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-Non-polymers , 4 types, 213 molecules
#3: Chemical | ChemComp-ZN / | ||
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#4: Chemical | ChemComp-CL / | ||
#5: Chemical | #6: 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: 2.3 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20%(w/v) PEG6K, 0.1M Tris pH8.0, 0.2M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.28229 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28229 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→69.07 Å / Num. obs: 24465 / % possible obs: 99.5 % / Redundancy: 16.9 % / CC1/2: 1 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.019 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.82→1.87 Å / Redundancy: 17 % / Rmerge(I) obs: 3.048 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1806 / CC1/2: 0.574 / Rpim(I) all: 0.757 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→42.739 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→42.739 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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