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Yorodumi- PDB-6nq7: Crystal structure of YetJ from Bacillus Subtilis crystallized in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nq7 | ||||||
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Title | Crystal structure of YetJ from Bacillus Subtilis crystallized in lipidic cubic phase | ||||||
Components | Uncharacterized protein YetJ | ||||||
Keywords | MEMBRANE PROTEIN / Ca2+ channel structure / closed state / 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 / GADOLINIUM ATOM / Uncharacterized protein YetJ Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Guo, G. / Chang, Y. / Liu, Q. | ||||||
Citation | Journal: Structure / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nq7.cif.gz | 54.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nq7.ent.gz | 37.2 KB | Display | PDB format |
PDBx/mmJSON format | 6nq7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nq7_validation.pdf.gz | 416.7 KB | Display | wwPDB validaton report |
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Full document | 6nq7_full_validation.pdf.gz | 416.8 KB | Display | |
Data in XML | 6nq7_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 6nq7_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/6nq7 ftp://data.pdbj.org/pub/pdb/validation_reports/nq/6nq7 | HTTPS FTP |
-Related structure data
Related structure data | 6nq8C 6nq9C 4pgrS 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: 23313.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: yetJ, BSU07200 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: O31539 |
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#2: Chemical | ChemComp-GD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.57 % |
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Crystal grow | Temperature: 298 K / Method: lipidic cubic phase / pH: 8 Details: 0.1 M Tris, pH 7.8, 5% PGA-LM (w/v), and 30% PEG 400 (v/v) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→47.22 Å / Num. obs: 6634 / % possible obs: 95.3 % / Redundancy: 7 % / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.5→2.63 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PGR Resolution: 2.5→47.22 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.898 / SU B: 12.076 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R Free: 0.343 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.99 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→47.22 Å
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Refine LS restraints |
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