+Open data
-Basic information
Entry | Database: PDB / ID: 5i5h | |||||||||
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Title | Ecoli global domain 245-586 | |||||||||
Components | Inner membrane protein YejM | |||||||||
Keywords | MEMBRANE PROTEIN / Ecoli 245-586 | |||||||||
Function / homology | Inner membrane protein YejM / Inner membrane protein YejM, N-terminal / Domain of unknown function (DUF3413) / sulfuric ester hydrolase activity / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / plasma membrane / Inner membrane protein YejM Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||
Authors | Dong, C. / Dong, H. | |||||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Structural insights into cardiolipin transfer from the Inner membrane to the outer membrane by PbgA in Gram-negative bacteria. Authors: Dong, H. / Zhang, Z. / Tang, X. / Huang, S. / Li, H. / Peng, B. / Dong, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i5h.cif.gz | 171.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i5h.ent.gz | 133.2 KB | Display | PDB format |
PDBx/mmJSON format | 5i5h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/5i5h ftp://data.pdbj.org/pub/pdb/validation_reports/i5/5i5h | HTTPS FTP |
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-Related structure data
Related structure data | 5i5dSC 5i5fC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 67364.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: yejM, yejN, b2188, JW2176 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AD27 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 310 K / Method: vapor diffusion, sitting drop / pH: 4.3 Details: 0.2 M lithium sulphate, 0.1 M sodium acetate pH 4.3 and 48% PEG400 PH range: 4.0-4.6 |
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-Data collection
Diffraction | Mean temperature: 193 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9798 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→47.83 Å / % possible obs: 99.6 % / Redundancy: 9.6 % / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 9.6 % / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5I5D Resolution: 1.65→47.7 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.04 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.023 / 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: 39.212 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→47.7 Å
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Refine LS restraints |
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