+Open data
-Basic information
Entry | Database: PDB / ID: 6l80 | ||||||
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Title | Crystal structure of pombe Mod21 N-terminus and Mozart1 | ||||||
Components |
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Keywords | TRANSLATION / gamma tubulin complex / microprotien / microtubule | ||||||
Function / homology | Function and homology information gamma-tubulin small complex => GO:0008275 / gamma-tubulin small complex => GO:0008275 / gamma-tubulin ring complex => GO:0000931 / inner plaque of mitotic spindle pole body / microtubule nucleation by spindle pole body / microtubule nucleation by interphase microtubule organizing center / gamma-tubulin complex localization / mitotic spindle pole body / equatorial microtubule organizing center / interphase microtubule organizing center ...gamma-tubulin small complex => GO:0008275 / gamma-tubulin small complex => GO:0008275 / gamma-tubulin ring complex => GO:0000931 / inner plaque of mitotic spindle pole body / microtubule nucleation by spindle pole body / microtubule nucleation by interphase microtubule organizing center / gamma-tubulin complex localization / mitotic spindle pole body / equatorial microtubule organizing center / interphase microtubule organizing center / gamma-tubulin complex / division septum assembly / mitotic spindle assembly / spindle / microtubule / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.00049753238 Å | ||||||
Authors | Huang, T.L. / Wang, H.J. / Wang, S.W. / Hsia, K.C. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Cell Rep / Year: 2020 Title: Promiscuous Binding of Microprotein Mozart1 to gamma-Tubulin Complex Mediates Specific Subcellular Targeting to Control Microtubule Array Formation. Authors: Huang, T.L. / Wang, H.J. / Chang, Y.C. / Wang, S.W. / Hsia, K.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l80.cif.gz | 167.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l80.ent.gz | 111.5 KB | Display | PDB format |
PDBx/mmJSON format | 6l80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l80_validation.pdf.gz | 451.2 KB | Display | wwPDB validaton report |
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Full document | 6l80_full_validation.pdf.gz | 454.9 KB | Display | |
Data in XML | 6l80_validation.xml.gz | 14 KB | Display | |
Data in CIF | 6l80_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/6l80 ftp://data.pdbj.org/pub/pdb/validation_reports/l8/6l80 | HTTPS FTP |
-Related structure data
-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: 12937.141 Da / Num. of mol.: 2 / Fragment: N-terminus Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: mod21, SPAC806.08c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UT52 #2: Protein | Mass: 11308.884 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: mzt1, tam4, SPAC9G1.15c / Production host: Escherichia coli (E. coli) / References: UniProt: P0CF96*PLUS #3: Water | ChemComp-HOH / | Sequence details | First 3 residues (G,P, and H) from the provided sequence of chain B/D are expression tag of the protein. | |
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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: 2.21 Å3/Da / Density % sol: 44.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 60% v/v Tacsimate pH 7.0, 0.1 M Bis-Tris propane pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 267023 / % possible obs: 99.8 % / Redundancy: 8.9 % / Biso Wilson estimate: 23.3077560766 Å2 / CC1/2: 0.995 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 2→2.05 Å / Num. unique obs: 29883 / CC1/2: 0.927 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.00049753238→29.5263043086 Å / SU ML: 0.208899365849 / Cross valid method: FREE R-VALUE / σ(F): 1.33785732234 / Phase error: 22.6560892751 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.0801219207 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.00049753238→29.5263043086 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: 41.8997806617 Å / Origin y: 41.3625837428 Å / Origin z: 47.1580100255 Å
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Refinement TLS group | Selection details: all |