+Open data
-Basic information
Entry | Database: PDB / ID: 2qa5 | ||||||
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Title | Crystal structure of Sept2 G-domain | ||||||
Components | Septin-2 | ||||||
Keywords | CELL CYCLE / STRUCTURAL PROTEIN / Septin2-GDP / biological dimer / Cell division / GTP-binding / Nucleotide-binding / Phosphorylation | ||||||
Function / homology | Function and homology information sperm annulus / septin complex / photoreceptor connecting cilium / cytoskeleton-dependent cytokinesis / septin ring / regulation of exocytosis / non-motile cilium / ciliary membrane / smoothened signaling pathway / intercellular bridge ...sperm annulus / 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 / cilium assembly / Anchoring of the basal body to the plasma membrane / kinetochore / spindle / microtubule cytoskeleton / actin cytoskeleton / synaptic vesicle / midbody / spermatogenesis / molecular adaptor activity / cell differentiation / cadherin binding / GTPase activity / GTP binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å | ||||||
Authors | Sirajuddin, M. / Wittinghofer, A. | ||||||
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 | 2qa5.cif.gz | 100.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qa5.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 2qa5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qa5_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2qa5_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2qa5_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 2qa5_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/2qa5 ftp://data.pdbj.org/pub/pdb/validation_reports/qa/2qa5 | 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 dimer. |
-Components
#1: Protein | Mass: 36536.062 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: BL21 / Gene: SEPT2, DIFF6, KIAA0158, NEDD5 / Plasmid: pGex6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL31 / References: UniProt: Q15019 #2: Chemical | |
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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: 2.6 Å3/Da / Density % sol: 52.67 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 5% PEG 6000, 0.1M BICINE, pH 9.0, 0.1M Glycine, 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: 0.9792 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 25, 2005 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→20 Å / Num. obs: 10431 / Redundancy: 5.4 % |
Reflection shell | Resolution: 3.4→3.5 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 14 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.4→19.79 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.834 / SU B: 33.699 / SU ML: 0.559 / Cross valid method: THROUGHOUT / ESU R Free: 0.655 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 81.54 Å2
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Refinement step | Cycle: LAST / Resolution: 3.4→19.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.486 Å / Total num. of bins used: 20
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