+Open data
-Basic information
Entry | Database: PDB / ID: 7pgf | ||||||||||||
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Title | Calcium-selective Sp1 channel pore domain only | ||||||||||||
Components | Ion transporter | ||||||||||||
Keywords | MEMBRANE PROTEIN / ion channel membrane protein transport protein antibody complex | ||||||||||||
Function / homology | : Function and homology information | ||||||||||||
Biological species | Ruegeria pomeroyi (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.5 Å | ||||||||||||
Authors | Lolicato, M. / Arrigoni, C. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2022 Title: Quaternary structure independent folding of voltage-gated ion channel pore domain subunits. Authors: Arrigoni, C. / Lolicato, M. / Shaya, D. / Rohaim, A. / Findeisen, F. / Fong, L.K. / Colleran, C.M. / Dominik, P. / Kim, S.S. / Schuermann, J.P. / DeGrado, W.F. / Grabe, M. / Kossiakoff, A.A. / Minor Jr., D.L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pgf.cif.gz | 76.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pgf.ent.gz | 48 KB | Display | PDB format |
PDBx/mmJSON format | 7pgf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pgf_validation.pdf.gz | 430.8 KB | Display | wwPDB validaton report |
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Full document | 7pgf_full_validation.pdf.gz | 437 KB | Display | |
Data in XML | 7pgf_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 7pgf_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/7pgf ftp://data.pdbj.org/pub/pdb/validation_reports/pg/7pgf | HTTPS FTP |
-Related structure data
Related structure data | 7pg8C 7pgbC 7pggC 7pghC 7pgiC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 15512.957 Da / Num. of mol.: 2 / Mutation: E56D, S57D, M60D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruegeria pomeroyi (bacteria) / Gene: HW563_01415 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7Y7EFG5 |
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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: 5.43 Å3/Da / Density % sol: 77.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: CaVSp1p purified in DM was concentrated to 13 mg mL-1 and reconstituted in bicelles prior crystallization to a final bicelle concentration of 8%. Native crystals grew in 25% PEG4000, 200 mM ...Details: CaVSp1p purified in DM was concentrated to 13 mg mL-1 and reconstituted in bicelles prior crystallization to a final bicelle concentration of 8%. Native crystals grew in 25% PEG4000, 200 mM MgCl2, 100 mM MES, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Oct 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 9000 / % possible obs: 97.17 % / Redundancy: 11.5 % / Biso Wilson estimate: 139.32 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.156 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 3.5→3.622 Å / Rmerge(I) obs: 1 / Num. unique obs: 879 / CC1/2: 0.126 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.5→14.93 Å / SU ML: 0.5953 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.3678 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 153.64 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→14.93 Å
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Refine LS restraints |
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LS refinement shell |
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