+Open data
-Basic information
Entry | Database: PDB / ID: 2qag | ||||||
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Title | Crystal structure of human septin trimer 2/6/7 | ||||||
Components |
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Keywords | CELL CYCLE / STRUCTURAL PROTEIN / Cell division / GTP-binding / Nucleotide-binding / Phosphorylation / Acetylation / Alternative splicing / Coiled coil | ||||||
Function / homology | Function and homology information septin collar / regulation of embryonic cell shape / sperm annulus / positive regulation of non-motile cilium assembly / septin complex / photoreceptor connecting cilium / cytoskeleton-dependent cytokinesis / septin ring / regulation of exocytosis / non-motile cilium ...septin collar / regulation of embryonic cell shape / sperm annulus / positive regulation of non-motile cilium assembly / septin complex / photoreceptor connecting cilium / cytoskeleton-dependent cytokinesis / septin ring / regulation of exocytosis / non-motile cilium / ciliary membrane / smoothened signaling pathway / intercellular bridge / cell division site / axoneme / cleavage furrow / mitotic cytokinesis / cilium assembly / axon terminus / stress fiber / Anchoring of the basal body to the plasma membrane / MAPK6/MAPK4 signaling / kinetochore / spindle / microtubule cytoskeleton / actin cytoskeleton / synaptic vesicle / midbody / spermatogenesis / molecular adaptor activity / cell differentiation / cadherin binding / GTPase activity / GTP binding / structural molecule activity / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 4 Å | ||||||
Authors | Sirajuddin, M. | ||||||
Citation | Journal: Nature / Year: 2007 Title: Structural insight into filament formation by mammalian septins. Authors: Sirajuddin, M. / Farkasovsky, M. / Hauer, F. / Kuhlmann, D. / Macara, I.G. / Weyand, M. / Stark, H. / Wittinghofer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qag.cif.gz | 150.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qag.ent.gz | 103.9 KB | Display | PDB format |
PDBx/mmJSON format | 2qag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qag_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2qag_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2qag_validation.xml.gz | 37.5 KB | Display | |
Data in CIF | 2qag_validation.cif.gz | 49 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/2qag ftp://data.pdbj.org/pub/pdb/validation_reports/qa/2qag | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a hexamer, but hexamer is divided by crystallographic symmetry, trimer occupies the asymmetric unit. Trimer model was generated from Sept2 (2QA5, submitted recently). |
-Components
#1: Protein | Mass: 41550.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SEPT2, DIFF6, KIAA0158, NEDD5 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta BL21 / References: UniProt: Q15019 | ||
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#2: Protein | Mass: 48948.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SEPT6, KIAA0128, SEP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14141 | ||
#3: Protein | Mass: 48837.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SEPT7, CDC10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16181 | ||
#4: Chemical | #5: Chemical | ChemComp-GTP / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 8.95 Å3/Da / Density % sol: 86.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.4M Ammonium Sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.07188 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 21, 2006 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07188 Å / Relative weight: 1 |
Reflection | Resolution: 4→50 Å / Num. obs: 42485 / Redundancy: 16.2 % / Rsym value: 0.229 / Net I/σ(I): 11.42 |
Reflection shell | Resolution: 4→4.1 Å / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 3.98 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 4→49.15 Å / Cor.coef. Fo:Fc: 0.796 / Cor.coef. Fo:Fc free: 0.787 / SU B: 82.738 / SU ML: 0.616 / Cross valid method: THROUGHOUT / ESU R: 0.7 / ESU R Free: 0.54 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Sept6 (Chain B) and Sept7 (Chain C) will have poly-alanine stretches due low resolution.
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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 mean: 78.174 Å2
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Refinement step | Cycle: LAST / Resolution: 4→49.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4→4.103 Å / Total num. of bins used: 20
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