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Yorodumi- PDB-4y7k: Structure of an archaeal mechanosensitive channel in closed state -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y7k | |||||||||
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Title | Structure of an archaeal mechanosensitive channel in closed state | |||||||||
Components | Large conductance mechanosensitive channel protein,Riboflavin synthase | |||||||||
Keywords | MEMBRANE PROTEIN / TRANSPORT PROTEIN / mechanosensitive channel / mechanosensation | |||||||||
Function / homology | Function and homology information riboflavin synthase / riboflavin synthase activity / riboflavin synthase complex / mechanosensitive monoatomic ion channel activity / riboflavin biosynthetic process / monoatomic ion transport / membrane Similarity search - Function | |||||||||
Biological species | Methanosarcina acetivorans C2A (archaea) Methanocaldococcus jannaschii DSM 2661 (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | |||||||||
Authors | Li, J. / Liu, Z. | |||||||||
Funding support | China, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Mechanical coupling of the multiple structural elements of the large-conductance mechanosensitive channel during expansion Authors: Li, J. / Guo, J. / Ou, X. / Zhang, M. / Li, Y. / Liu, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y7k.cif.gz | 237.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y7k.ent.gz | 191.3 KB | Display | PDB format |
PDBx/mmJSON format | 4y7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/4y7k ftp://data.pdbj.org/pub/pdb/validation_reports/y7/4y7k | HTTPS FTP |
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-Related structure data
Related structure data | 4y7jC 2b98S 2oarS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 30608.977 Da / Num. of mol.: 5 / Mutation: K101 deletion Source method: isolated from a genetically manipulated source Details: chimera of Large conductance mechanosensitive channel protein and Riboflavin synthase Source: (gene. exp.) Methanosarcina acetivorans C2A (archaea), (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea) Strain: C2A, DSM 2661 / Gene: MA_2285, ribC, MJ1184 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q8TNK0, UniProt: Q58584 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 70.06 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.3 / Details: 7% PEG4000, 0.4M NH4SCN, 0.1M Citric acid(pH7.3) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. all: 27942 / Num. obs: 27942 / % possible obs: 99.2 % / Redundancy: 11 % / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 3.5→3.63 Å / Redundancy: 11.2 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OAR, 2B98 Resolution: 3.5→42 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.935 / SU B: 50.294 / SU ML: 0.709 / Cross valid method: THROUGHOUT / ESU R Free: 0.596 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 170.97 Å2
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Refinement step | Cycle: LAST / Resolution: 3.5→42 Å
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Refine LS restraints |
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