+Open data
-Basic information
Entry | Database: PDB / ID: 5aji | ||||||
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Title | MscS D67R1 high resolution | ||||||
Components | SMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL | ||||||
Keywords | TRANSPORT PROTEIN | ||||||
Function / homology | Function and homology information intracellular water homeostasis / mechanosensitive monoatomic ion channel activity / monoatomic ion transmembrane transport / protein homooligomerization / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å | ||||||
Authors | Naismith, J.H. / Pliotas, C. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2015 Title: The Role of Lipids in Mechanosensation. Authors: Pliotas, C. / Dahl, A.C.E. / Rasmussen, T. / Mahendran, K.R. / Smith, T.K. / Marius, P. / Gault, J. / Banda, T. / Rasmussen, A. / Miller, S. / Robinson, C.V. / Bayley, H. / Sansom, M.S.P. / ...Authors: Pliotas, C. / Dahl, A.C.E. / Rasmussen, T. / Mahendran, K.R. / Smith, T.K. / Marius, P. / Gault, J. / Banda, T. / Rasmussen, A. / Miller, S. / Robinson, C.V. / Bayley, H. / Sansom, M.S.P. / Booth, I.R. / Naismith, J.H. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 35-STRANDED BARREL THIS IS REPRESENTED BY A 36-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5aji.cif.gz | 699.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aji.ent.gz | 598 KB | Display | PDB format |
PDBx/mmJSON format | 5aji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5aji_validation.pdf.gz | 518.2 KB | Display | wwPDB validaton report |
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Full document | 5aji_full_validation.pdf.gz | 541.4 KB | Display | |
Data in XML | 5aji_validation.xml.gz | 62.3 KB | Display | |
Data in CIF | 5aji_validation.cif.gz | 80.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/5aji ftp://data.pdbj.org/pub/pdb/validation_reports/aj/5aji | HTTPS FTP |
-Related structure data
Related structure data | 4ageS S: Starting model for refinement |
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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: 31095.234 Da / Num. of mol.: 7 / Mutation: YES Source method: isolated from a genetically manipulated source Details: THE PROTEIN IS SPIN LABELED ON D67C. / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0C0S2, UniProt: P0C0S1*PLUS #2: Chemical | #3: Chemical | ChemComp-HEX / #4: Chemical | |
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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: 3.76 Å3/Da / Density % sol: 67.29 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 |
Detector | Date: Jan 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→64 Å / Num. obs: 66747 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.99→3.07 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.002 / Mean I/σ(I) obs: 1.1 / % possible all: 99.8 |
-Processing
Software | Name: REFMAC / Version: 5.8.0073 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4AGE Resolution: 2.99→68.51 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.911 / SU B: 50.987 / SU ML: 0.373 / Cross valid method: THROUGHOUT / ESU R: 1.017 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED A HIGHER RESOLUTION VERSION OF 4AGE
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 114.531 Å2
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Refinement step | Cycle: LAST / Resolution: 2.99→68.51 Å
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Refine LS restraints |
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