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Yorodumi- PDB-4kjr: Crystal structure of selenium substituted Ca2+/H+ antiporter prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kjr | ||||||
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Title | Crystal structure of selenium substituted Ca2+/H+ antiporter proteinYfkE | ||||||
Components | cation exchanger YfkE | ||||||
Keywords | TRANSPORT PROTEIN / Ca/H+ antiporter / YfkE | ||||||
Function / homology | Function and homology information calcium:proton antiporter activity / calcium ion transmembrane transport / intracellular calcium ion homeostasis / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å | ||||||
Authors | Wu, M. / Tong, S. / Zheng, L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Crystal structure of Ca2+/H+ antiporter protein YfkE reveals the mechanisms of Ca2+ efflux and its pH regulation. Authors: Wu, M. / Tong, S. / Waltersperger, S. / Diederichs, K. / Wang, M. / Zheng, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kjr.cif.gz | 125.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kjr.ent.gz | 105.5 KB | Display | PDB format |
PDBx/mmJSON format | 4kjr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kjr_validation.pdf.gz | 448.7 KB | Display | wwPDB validaton report |
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Full document | 4kjr_full_validation.pdf.gz | 499.5 KB | Display | |
Data in XML | 4kjr_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 4kjr_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/4kjr ftp://data.pdbj.org/pub/pdb/validation_reports/kj/4kjr | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38111.816 Da / Num. of mol.: 2 / Mutation: L77M,K116A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Strain: 168 / Gene: yfkE, BSU07920 / Production host: Escherichia coli (E. coli) / References: UniProt: O34840 #2: 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 | Density Matthews: 3.49 Å3/Da / Density % sol: 64.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 23-25% PEG400, 0.2M Ammonium Sulfate, 20mM NaCl, 0.1M NaAc pH4.0, 3% Hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9790, 0.9792, 0.9641 | |||||||||||||||
Detector | Type: NOIR-1 / Detector: CCD / Date: Apr 13, 2011 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection twin |
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Reflection | Resolution: 2.9→85.16 Å / Num. all: 22757 / Num. obs: 22530 / % possible obs: 99.9 % / Observed criterion σ(I): 17.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3→85.16 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.926 / SU B: 26.818 / SU ML: 0.424 / Cross valid method: THROUGHOUT / ESU R: 0.496 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 92.017 Å2
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Refinement step | Cycle: LAST / Resolution: 3→85.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.998→3.076 Å / Total num. of bins used: 20
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