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Open data
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Basic information
Entry | Database: PDB / ID: 6nq8 | ||||||
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Title | Crystal structure of YetJ mutant from Bacillus Subtilis - D171E | ||||||
![]() | Uncharacterized protein YetJ | ||||||
![]() | MEMBRANE PROTEIN / Ca2+ channel structure / open conformation / pH sensor | ||||||
Function / homology | Bax inhibitor 1-related / Inhibitor of apoptosis-promoting Bax1 / calcium channel activity / calcium ion transport / negative regulation of apoptotic process / membrane / plasma membrane / Uncharacterized protein YetJ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guo, G. / Chang, Y. / Liu, Q. | ||||||
![]() | ![]() Title: Ion and pH Sensitivity of a TMBIM Ca2+Channel. Authors: Guo, G. / Xu, M. / Chang, Y. / Luyten, T. / Seitaj, B. / Liu, W. / Zhu, P. / Bultynck, G. / Shi, L. / Quick, M. / Liu, Q. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.7 KB | Display | ![]() |
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PDB format | ![]() | 131.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.5 KB | Display | ![]() |
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Full document | ![]() | 439.4 KB | Display | |
Data in XML | ![]() | 26 KB | Display | |
Data in CIF | ![]() | 35.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nq7C ![]() 6nq9C ![]() 4pgsS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23858.578 Da / Num. of mol.: 4 / Mutation: D171E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: yetJ, BSU07200 Production host: ![]() ![]() References: UniProt: O31539 |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M MOPS, pH 7.5, 38% PEG 400, and 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→47.15 Å / Num. obs: 76248 / % possible obs: 99.1 % / Redundancy: 3.2 % / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 3.1→3.31 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4PGS Resolution: 3.1→39.082 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.57
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→39.082 Å
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Refine LS restraints |
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LS refinement shell |
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