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Yorodumi- PDB-4g7y: Crystal structure of voltage sensing domain of Ci-VSP with fragme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g7y | ||||||
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Title | Crystal structure of voltage sensing domain of Ci-VSP with fragment antibody (R217E, 2.8 A) | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / alpha helix / fragment antibody / Voltage sensing domain / Sensing voltage | ||||||
Function / homology | Function and homology information regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / phosphatidylinositol dephosphorylation / protein tyrosine phosphatase activity / cell projection / cell motility / monoatomic ion channel activity / negative regulation of cell population proliferation / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Ciona intestinalis (vase tunicate) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Li, Q. | ||||||
Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2014 Title: Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain. Authors: Li, Q. / Wanderling, S. / Paduch, M. / Medovoy, D. / Singharoy, A. / McGreevy, R. / Villalba-Galea, C.A. / Hulse, R.E. / Roux, B. / Schulten, K. / Kossiakoff, A. / Perozo, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g7y.cif.gz | 118.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g7y.ent.gz | 95.6 KB | Display | PDB format |
PDBx/mmJSON format | 4g7y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4g7y_validation.pdf.gz | 455.7 KB | Display | wwPDB validaton report |
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Full document | 4g7y_full_validation.pdf.gz | 461.7 KB | Display | |
Data in XML | 4g7y_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 4g7y_validation.cif.gz | 30 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/4g7y ftp://data.pdbj.org/pub/pdb/validation_reports/g7/4g7y | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules S
#3: Protein | Mass: 21168.658 Da / Num. of mol.: 1 / Mutation: R217E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ciona intestinalis (vase tunicate) / Gene: Ci-VSP / Plasmid: pQE32 with sequence encoding for Ci-VSD / Production host: Escherichia coli (E. coli) / Strain (production host): XL10-Gold / References: UniProt: Q4W8A1 |
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-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 23092.639 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Plasmid: phagemid coding for both heavy chain and light chain of the fragment antibody Production host: Escherichia coli (E. coli) / Strain (production host): 55244 |
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#2: Antibody | Mass: 23103.670 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Plasmid: phagemid coding for both heavy chain and light chain of the fragment antibody Production host: Escherichia coli (E. coli) / Strain (production host): 55244 |
-Non-polymers , 4 types, 38 molecules
#4: Chemical | ChemComp-CL / |
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#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-LDA / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 65.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.1 M Bicine, 0.3 M MgCl2, 24% PEG 2000, 10% Glycerol, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.8→104.8 Å / Num. all: 24429 / Num. obs: 24429 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.2 / Redundancy: 8.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→104.8 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.896 / SU B: 11.674 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.474 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 57.094 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→104.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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