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Yorodumi- PDB-8sjj: X-ray structure of the metastable SEPT14-SEPT7 heterodimeric coil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8sjj | |||||||||
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Title | X-ray structure of the metastable SEPT14-SEPT7 heterodimeric coiled coil | |||||||||
Components |
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Keywords | CELL CYCLE / Septin / Coiled coil | |||||||||
Function / homology | Function and homology information protein localization to perinuclear region of cytoplasm / septin complex / cytoskeleton-dependent cytokinesis / septin ring / motile cilium / cell division site / cleavage furrow / spermatid development / acrosomal vesicle / neuron migration ...protein localization to perinuclear region of cytoplasm / septin complex / cytoskeleton-dependent cytokinesis / septin ring / motile cilium / cell division site / cleavage furrow / spermatid development / acrosomal vesicle / neuron migration / kinetochore / spindle / microtubule cytoskeleton / midbody / spermatogenesis / perikaryon / molecular adaptor activity / cytoskeleton / axon / GTPase activity / dendrite / GTP binding / perinuclear region of cytoplasm / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.781 Å | |||||||||
Authors | Cavini, I.A. / Pereira, H.M. / Garratt, R.C. | |||||||||
Funding support | Brazil, 2items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2023 Title: X-ray structure of the metastable SEPT14-SEPT7 coiled coil reveals a hendecad region crucial for heterodimerization. Authors: Cavini, I.A. / Winter, A.J. / D'Muniz Pereira, H. / Woolfson, D.N. / Crump, M.P. / Garratt, R.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sjj.cif.gz | 152.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sjj.ent.gz | 118.7 KB | Display | PDB format |
PDBx/mmJSON format | 8sjj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sjj_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 8sjj_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 8sjj_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 8sjj_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/8sjj ftp://data.pdbj.org/pub/pdb/validation_reports/sj/8sjj | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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: 9249.529 Da / Num. of mol.: 2 / Fragment: coiled coil domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SEPTIN14, SEPT14 / Plasmid: pETSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q6ZU15 #2: Protein | Mass: 10935.504 Da / Num. of mol.: 2 / Fragment: residues 307-390 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pETSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A023T695 #3: Chemical | ChemComp-NA / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.01 Å3/Da / Density % sol: 38.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M Bis-Tris pH 5.0, 24% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 25, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.781→91.294 Å / Num. obs: 22355 / % possible obs: 72.47 % / Redundancy: 6.83 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.041 / Rrim(I) all: 0.108 / Net I/σ(I): 10.602 |
Reflection shell | Resolution: 1.781→1.996 Å / Rmerge(I) obs: 1.168 / Mean I/σ(I) obs: 1.29 / Num. unique obs: 1118 / CC1/2: 0.5692 / Rpim(I) all: 0.535 / Rrim(I) all: 1.1289 / % possible all: 14.18 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.781→91.29 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.881 / SU R Cruickshank DPI: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.241 / SU Rfree Blow DPI: 0.208 / SU Rfree Cruickshank DPI: 0.204
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Displacement parameters | Biso mean: 32.76 Å2
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Refine analyze | Luzzati coordinate error obs: 0.31 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.781→91.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.781→1.9 Å
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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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