+Open data
-Basic information
Entry | Database: PDB / ID: 3t5d | ||||||
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Title | Crystal structure of Septin 7 in complex with GDP | ||||||
Components | Septin-7 | ||||||
Keywords | SIGNALING PROTEIN / GTP-binding protein / cytoskeleton | ||||||
Function / homology | Function and homology information regulation of embryonic cell shape / sperm annulus / positive regulation of non-motile cilium assembly / septin complex / cytoskeleton-dependent cytokinesis / septin ring / non-motile cilium / cell division site / axoneme / cleavage furrow ...regulation of embryonic cell shape / sperm annulus / positive regulation of non-motile cilium assembly / septin complex / cytoskeleton-dependent cytokinesis / septin ring / non-motile cilium / cell division site / axoneme / cleavage furrow / cilium assembly / stress fiber / MAPK6/MAPK4 signaling / kinetochore / spindle / microtubule cytoskeleton / midbody / spermatogenesis / molecular adaptor activity / cell differentiation / cadherin binding / GTPase activity / GTP binding / structural molecule activity / extracellular exosome / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Zent, E. / Wittinghofer, A. | ||||||
Citation | Journal: Biol.Chem. / Year: 2011 Title: Structural and biochemical properties of Sept7, a unique septin required for filament formation. Authors: Zent, E. / Vetter, I. / Wittinghofer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t5d.cif.gz | 105.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t5d.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 3t5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/3t5d ftp://data.pdbj.org/pub/pdb/validation_reports/t5/3t5d | 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 2 / Auth seq-ID: 30 - 295 / Label seq-ID: 7 - 272
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-Components
#1: Protein | Mass: 31349.900 Da / Num. of mol.: 2 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 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 3.29 Å3/Da / Density % sol: 62.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 0.2M sodium chlorid, 1.1M ammonium sulfate, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99986 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99986 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→71.25 Å / Num. all: 12190 / Num. obs: 12079 / % possible obs: 99.1 % / Redundancy: 8.9 % |
Reflection shell | Resolution: 3.3→3.4 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 3.85 / Num. unique all: 1007 / Rsym value: 0.596 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→71.25 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.86 / SU B: 86.942 / SU ML: 0.653 / Cross valid method: THROUGHOUT / ESU R Free: 0.619 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 68.02 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→71.25 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.3→3.386 Å / Total num. of bins used: 20
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