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Yorodumi- PDB-4g80: Crystal structure of voltage sensing domain of Ci-VSP with fragme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g80 | ||||||
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Title | Crystal structure of voltage sensing domain of Ci-VSP with fragment antibody (WT, 3.8 A) | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / alpha helix / fragment antibody / voltage sensing domain / sensing voltage | ||||||
Function / homology | Function and homology information phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / phosphatidylinositol dephosphorylation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / dephosphorylation / protein tyrosine phosphatase activity / cell projection / cell motility / monoatomic ion channel activity / negative regulation of cell population proliferation / membrane ...phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / phosphatidylinositol dephosphorylation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / dephosphorylation / protein tyrosine phosphatase activity / cell projection / cell motility / monoatomic ion channel activity / negative regulation of cell population proliferation / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Ciona intestinalis (vase tunicate) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.58 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 | 4g80.cif.gz | 433.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g80.ent.gz | 366.1 KB | Display | PDB format |
PDBx/mmJSON format | 4g80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4g80_validation.pdf.gz | 518.6 KB | Display | wwPDB validaton report |
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Full document | 4g80_full_validation.pdf.gz | 560.7 KB | Display | |
Data in XML | 4g80_validation.xml.gz | 78.4 KB | Display | |
Data in CIF | 4g80_validation.cif.gz | 104.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/4g80 ftp://data.pdbj.org/pub/pdb/validation_reports/g8/4g80 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 17750.729 Da / Num. of mol.: 4 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, UniProt: F6XHE4*PLUS #2: Antibody | Mass: 23988.711 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Plasmid: phagemid coding for both heavy and light chain of the fragment antibody Production host: Escherichia coli (E. coli) / Strain (production host): 55244 #3: Antibody | Mass: 22989.506 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Plasmid: phagemid coding for both heavy and light chain of the fragment antibody Production host: Escherichia coli (E. coli) / Strain (production host): 55244 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 40 |
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-Sample preparation
Crystal | Density Matthews: 5.1 Å3/Da / Density % sol: 75.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Na Citrate, 0.1 M Li2SO4, 20% PEG 1000, 10% glycerol, pH 5.5, 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: 3.58→50 Å / Num. all: 55790 / Num. obs: 55790 / % possible obs: 95.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rsym value: 0.144 / Net I/σ(I): 12.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.58→50 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.871 / SU B: 39.019 / SU ML: 0.555 / Cross valid method: THROUGHOUT / ESU R Free: 0.627 / 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: 149.865 Å2
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Refinement step | Cycle: LAST / Resolution: 3.58→50 Å
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Refine LS restraints |
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