+Open data
-Basic information
Entry | Database: PDB / ID: 6juh | ||||||
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Title | structure of CavAb in complex with efonidipine | ||||||
Components | Ion transport proteinIon transporter | ||||||
Keywords | MEMBRANE PROTEIN / voltage-gated Calcium channel block | ||||||
Function / homology | Function and homology information monoatomic cation channel activity / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Arcobacter butzleri RM4018 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Tang, L. / Xu, F. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2019 Title: Structural basis for efonidipine block of a voltage-gated Ca2+channel. Authors: Xu, F. / Xiong, W. / Huang, Y. / Shen, J. / Zhou, D. / Tang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6juh.cif.gz | 446.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6juh.ent.gz | 366.2 KB | Display | PDB format |
PDBx/mmJSON format | 6juh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/6juh ftp://data.pdbj.org/pub/pdb/validation_reports/ju/6juh | HTTPS FTP |
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-Related structure data
Related structure data | 4ms2S S: Starting model for refinement |
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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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 31090.836 Da / Num. of mol.: 4 / Mutation: E1177D, S1178D, M1181N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arcobacter butzleri RM4018 (bacteria) / Strain: RM4018 / Variant: RM4018 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5 |
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-Non-polymers , 5 types, 15 molecules
#2: Chemical | ChemComp-MC3 / #3: Chemical | ChemComp-PX4 / #4: Chemical | ChemComp-G3P / #5: Chemical | #6: Chemical | ChemComp-C9X / | |
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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: 6.11 Å3/Da / Density % sol: 79.86 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 1.0-2.0M Ammonium Sulfate 100 mM Na-citrate pH=5.0 |
-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: Apr 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. obs: 53912 / % possible obs: 89 % / Redundancy: 5 % / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 3→3.16 Å / Num. unique obs: 8310 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MS2 Resolution: 3→29.818 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→29.818 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -3.327 Å / Origin y: 30.9757 Å / Origin z: 32.4806 Å
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Refinement TLS group | Selection details: all |