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Yorodumi- PDB-5nuo: Structural basis for maintenance of bacterial outer membrane lipi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nuo | ||||||
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Title | Structural basis for maintenance of bacterial outer membrane lipid asymmetry | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Outer membrane / lipid asymmetry / lipoprotein / phospholipid translocation | ||||||
Function / homology | Function and homology information intermembrane phospholipid transfer / colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding ...intermembrane phospholipid transfer / colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / protein transport / monoatomic ion channel activity / lipid binding / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Abellon-Ruiz, J. / Kaptan, S.S. / Basle, A. / Claudi, B. / Bumann, D. / Kleinekathofer, U. / van den Berg, B. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Microbiol / Year: 2017 Title: Structural basis for maintenance of bacterial outer membrane lipid asymmetry. Authors: Abellon-Ruiz, J. / Kaptan, S.S. / Basle, A. / Claudi, B. / Bumann, D. / Kleinekathofer, U. / van den Berg, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nuo.cif.gz | 639.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nuo.ent.gz | 533.9 KB | Display | PDB format |
PDBx/mmJSON format | 5nuo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/5nuo ftp://data.pdbj.org/pub/pdb/validation_reports/nu/5nuo | HTTPS FTP |
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-Related structure data
Related structure data | 5nupC 5nuqC 5nurC 2zfgS 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: 37114.250 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: ompF, cmlB, coa, cry, tolF, b0929, JW0912 / Production host: Escherichia coli (E. coli) / References: UniProt: P02931 #2: Protein | Mass: 26364.527 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: mlaA, vacJ, AGG09_21815, BB749_07690, BCB67_11070, BL143_09030, BN49_3944, PMK1_00224, SAMEA3531778_01593, SM30_03044, SM57_02930 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0W8AQT6 #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-C8E / ( |
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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: 4.32 Å3/Da / Density % sol: 71.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.05 M sodium sulfate, 0.05 M lithium sulfate, 0.05 M Tris pH 8.5 and 35 % PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97886 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97886 Å / Relative weight: 1 |
Reflection | Resolution: 3.07→95.6 Å / Num. obs: 62533 / % possible obs: 99.7 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rpim(I) all: 0.048 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 3.07→3.12 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2880 / CC1/2: 0.895 / Rpim(I) all: 0.425 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZFG Resolution: 3.2→88.547 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.19
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→88.547 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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