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Yorodumi- PDB-6keb: Structure basis for Diltiazem block of a voltage-gated calcium channel -
+Open data
-Basic information
Entry | Database: PDB / ID: 6keb | ||||||||||||
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Title | Structure basis for Diltiazem block of a voltage-gated calcium channel | ||||||||||||
Components | Ion transport protein | ||||||||||||
Keywords | TRANSPORT PROTEIN / Tetrameric / Voltage-gated Ion Channel / Voltage-gated Calcium Channel Block / MEMBRANE PROTEIN | ||||||||||||
Function / homology | Function and homology information membrane depolarization during action potential / voltage-gated sodium channel complex / voltage-gated sodium channel activity / identical protein binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Arcobacter butzleri (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||||||||
Authors | Tang, L. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Mol.Pharmacol. / Year: 2019 Title: Structural Basis for Diltiazem Block of a Voltage-Gated Ca2+Channel. Authors: Tang, L. / Gamal El-Din, T.M. / Lenaeus, M.J. / Zheng, N. / Catterall, W.A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6keb.cif.gz | 203 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6keb.ent.gz | 158.5 KB | Display | PDB format |
PDBx/mmJSON format | 6keb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6keb_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 6keb_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 6keb_validation.xml.gz | 39.3 KB | Display | |
Data in CIF | 6keb_validation.cif.gz | 51.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/6keb ftp://data.pdbj.org/pub/pdb/validation_reports/ke/6keb | 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: 32980.801 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arcobacter butzleri (bacteria) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5 #2: Chemical | ChemComp-PX4 / #3: Chemical | #4: Chemical | ChemComp-D6C / [( | #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: 5.74 Å3/Da / Density % sol: 78.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: CHAPSO:DMPC BICELLES,0.1M Na-citrate,pH5.0,2M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.987 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 3.2→30 Å / Num. obs: 45703 / % possible obs: 90.5 % / Redundancy: 5.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.137 / Net I/σ(I): 9.8 | |||||||||||||||
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6686 / CC1/2: 0.813 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→29.85 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.836 / SU B: 12.206 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 245.66 Å2 / Biso mean: 84.033 Å2 / Biso min: 21.06 Å2
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Refinement step | Cycle: final / Resolution: 3.2→29.85 Å
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Refine LS restraints |
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