+Open data
-Basic information
Entry | Database: PDB / ID: 6wcu | |||||||||||||||
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Title | Crystal structure of coiled coil region of human septin 5 | |||||||||||||||
Components | Septin-5 | |||||||||||||||
Keywords | STRUCTURAL PROTEIN / Coiled coil / Septin | |||||||||||||||
Function / homology | Function and homology information protein localization => GO:0008104 / septin complex / synaptic vesicle targeting / cytoskeleton-dependent cytokinesis / septin ring / regulation of exocytosis / regulation of synaptic vesicle exocytosis / adult behavior / cell division site / social behavior ...protein localization => GO:0008104 / septin complex / synaptic vesicle targeting / cytoskeleton-dependent cytokinesis / septin ring / regulation of exocytosis / regulation of synaptic vesicle exocytosis / adult behavior / cell division site / social behavior / microtubule cytoskeleton / synaptic vesicle / molecular adaptor activity / GTPase activity / GTP binding / structural molecule activity / identical protein binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.8 Å | |||||||||||||||
Authors | Cabrejos, D.A.L. / Cavini, I. / Sala, F.A. / Valadares, N.F. / Pereira, H.M. / Brandao-Neto, J. / Nascimento, A.F.Z. / Uson, I. / Araujo, A.P.U. / Garratt, R.C. | |||||||||||||||
Funding support | Brazil, 4items
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Citation | Journal: J.Mol.Biol. / Year: 2021 Title: Orientational Ambiguity in Septin Coiled Coils and its Structural Basis. Authors: Leonardo, D.A. / Cavini, I.A. / Sala, F.A. / Mendonca, D.C. / Rosa, H.V.D. / Kumagai, P.S. / Crusca Jr., E. / Valadares, N.F. / Marques, I.A. / Brandao-Neto, J. / Munte, C.E. / Kalbitzer, H. ...Authors: Leonardo, D.A. / Cavini, I.A. / Sala, F.A. / Mendonca, D.C. / Rosa, H.V.D. / Kumagai, P.S. / Crusca Jr., E. / Valadares, N.F. / Marques, I.A. / Brandao-Neto, J. / Munte, C.E. / Kalbitzer, H.R. / Soler, N. / Uson, I. / Andre, I. / Araujo, A.P.U. / D'Muniz Pereira, H. / 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 | 6wcu.cif.gz | 38 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wcu.ent.gz | 27.4 KB | Display | PDB format |
PDBx/mmJSON format | 6wcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/6wcu ftp://data.pdbj.org/pub/pdb/validation_reports/wc/6wcu | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 3888.561 Da / Num. of mol.: 2 / Fragment: Coiled coil region / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99719 #2: 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: 1.67 Å3/Da / Density % sol: 26.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M citric acid pH 5.0, 1.6 M ammonium sulfate |
-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: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2011 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection twin | Operator: h,-k,-h-l / Fraction: 0.49 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→26.11 Å / Num. obs: 4769 / % possible obs: 97.4 % / Redundancy: 3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.04 / Rrim(I) all: 0.073 / Net I/σ(I): 11.3 / Num. measured all: 14437 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.8→22.465 Å / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.08
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.72 Å2 / Biso mean: 21.5542 Å2 / Biso min: 10.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→22.465 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2
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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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