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Yorodumi- PDB-5klb: Crystal structure of the CavAb voltage-gated calcium channel(wild... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5klb | |||||||||
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Title | Crystal structure of the CavAb voltage-gated calcium channel(wild-type, 2.7A) | |||||||||
Components | Ion transport proteinIon transporter | |||||||||
Keywords | TRANSPORT PROTEIN / Voltage-gated Calcium Channel | |||||||||
Function / homology | Function and homology information monoatomic cation channel activity / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Arcobacter butzleri (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Tang, L. / Gamal EL-Din, T.M. / Swanson, T.M. / Pryde, D.C. / Scheuer, T. / Zheng, N. / Catterall, W.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nature / Year: 2016 Title: Structural basis for inhibition of a voltage-gated Ca(2+) channel by Ca(2+) antagonist drugs. Authors: Tang, L. / El-Din, T.M. / Swanson, T.M. / Pryde, D.C. / Scheuer, T. / 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 | 5klb.cif.gz | 251.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5klb.ent.gz | 205.9 KB | Display | PDB format |
PDBx/mmJSON format | 5klb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/5klb ftp://data.pdbj.org/pub/pdb/validation_reports/kl/5klb | HTTPS FTP |
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-Related structure data
Related structure data | 5klgC 5klsC 5kmdC 5kmfC 5kmhC 4ms2S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 33112.000 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arcobacter butzleri (strain RM4018) (bacteria) Strain: RM4018 / Gene: Abu_1752 / Plasmid: pFASTBAC DUAL / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5 #2: Chemical | ChemComp-MC3 / #3: Chemical | #4: Chemical | ChemComp-CPS / #5: 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 grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: CHAPSO:DMPC BICELLES,0.1M Na-citrate,pH5.0,2M Ammonium Sulfate PH range: 4.7-5.3 |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 770488 / % possible obs: 92.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.984 / Mean I/σ(I) obs: 2.4 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MS2 Resolution: 2.7→29.932 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 27.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→29.932 Å
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Refine LS restraints |
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LS refinement shell |
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