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Yorodumi- PDB-3kvt: TETRAMERIZATION DOMAIN FROM AKV3.1 (SHAW-SUBFAMILY) VOLTAGE-GATED... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kvt | ||||||
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Title | TETRAMERIZATION DOMAIN FROM AKV3.1 (SHAW-SUBFAMILY) VOLTAGE-GATED POTASSIUM CHANNEL | ||||||
Components | POTASSIUM CHANNEL PROTEIN SHAW | ||||||
Keywords | POTASSIUM CHANNEL / TETRAMERIZATION DOMAIN / MOLECULAR RECOGNITION / ZINC-BINDING | ||||||
Function / homology | Function and homology information delayed rectifier potassium channel activity / neuronal cell body membrane / voltage-gated potassium channel complex / axon terminus / dendrite membrane / protein homooligomerization / presynaptic membrane / postsynaptic membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Aplysia californica (California sea hare) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Bixby, K.A. / Nanao, M.H. / Shen, N.V. / Kreusch, A. / Bellamy, H. / Pfaffinger, P.J. / Choe, S. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Zn2+-binding and molecular determinants of tetramerization in voltage-gated K+ channels. Authors: Bixby, K.A. / Nanao, M.H. / Shen, N.V. / Kreusch, A. / Bellamy, H. / Pfaffinger, P.J. / Choe, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kvt.cif.gz | 36.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kvt.ent.gz | 23.9 KB | Display | PDB format |
PDBx/mmJSON format | 3kvt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kvt_validation.pdf.gz | 359.9 KB | Display | wwPDB validaton report |
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Full document | 3kvt_full_validation.pdf.gz | 359.9 KB | Display | |
Data in XML | 3kvt_validation.xml.gz | 3.3 KB | Display | |
Data in CIF | 3kvt_validation.cif.gz | 4.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/3kvt ftp://data.pdbj.org/pub/pdb/validation_reports/kv/3kvt | 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
#1: Protein | Mass: 13389.151 Da / Num. of mol.: 1 / Fragment: TETRAMERIZATION (T1) DOMAIN / Mutation: A42G, L43M, A44L Source method: isolated from a genetically manipulated source Details: ONE ZN2+ PER MONOMER TETRAHEDRALLY COORDINATED AT MONOMER-MONOMER INTERFACE Source: (gene. exp.) Aplysia californica (California sea hare) Tissue: NERVE / Cell line: BL21 PLYS S / Cellular location: MEMBRANE / Plasmid: PET16B / Cell line (production host): BL21 PLYS S / Production host: Escherichia coli (E. coli) / Strain (production host): PET / References: UniProt: O76457 |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997 / Details: PLATINUM COATED MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 11135 / % possible obs: 99.8 % / Redundancy: 11.3 % / Biso Wilson estimate: 18.7 Å2 / Rsym value: 0.057 |
Reflection shell | Resolution: 2→2.07 Å / Rsym value: 0.401 / % possible all: 99.5 |
Reflection | *PLUS Num. measured all: 126110 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 99.5 % / Rmerge(I) obs: 0.401 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AP61 Resolution: 2→25 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 28.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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