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Yorodumi- PDB-5iv9: The LPS Transporter LptDE from Klebsiella pneumoniae, full-length -
+Open data
-Basic information
Entry | Database: PDB / ID: 5iv9 | ||||||
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Title | The LPS Transporter LptDE from Klebsiella pneumoniae, full-length | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / LptD / LptE / lipopolysaccharide / Transporter | ||||||
Function / homology | Function and homology information lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / : / cell outer membrane Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.369 Å | ||||||
Authors | Botos, I. / McCarthy, J.G. / Buchanan, S.K. | ||||||
Citation | Journal: Structure / Year: 2016 Title: Structural and Functional Characterization of the LPS Transporter LptDE from Gram-Negative Pathogens. Authors: Botos, I. / Majdalani, N. / Mayclin, S.J. / McCarthy, J.G. / Lundquist, K. / Wojtowicz, D. / Barnard, T.J. / Gumbart, J.C. / Buchanan, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5iv9.cif.gz | 186.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iv9.ent.gz | 153.7 KB | Display | PDB format |
PDBx/mmJSON format | 5iv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5iv9_validation.pdf.gz | 703.3 KB | Display | wwPDB validaton report |
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Full document | 5iv9_full_validation.pdf.gz | 711.4 KB | Display | |
Data in XML | 5iv9_validation.xml.gz | 33.5 KB | Display | |
Data in CIF | 5iv9_validation.cif.gz | 43.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/5iv9 ftp://data.pdbj.org/pub/pdb/validation_reports/iv/5iv9 | HTTPS FTP |
-Related 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: 85991.914 Da / Num. of mol.: 1 / Fragment: unp residues 25-782 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: imp, lptD / Production host: Escherichia coli (E. coli) / References: UniProt: C4T9I0 |
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#2: Protein | Mass: 19392.877 Da / Num. of mol.: 1 / Fragment: unp residues 20-196 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: lptE, APU20_03225 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J4W1Y0 |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.78 Å3/Da / Density % sol: 74.29 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 25% 1,2-propanediol, 100 mM phosphate-citrate pH 4.2, 10% glycerol, 5% PEG 3000 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 4.369→44.717 Å / Num. obs: 12420 / % possible obs: 95.6 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 14.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.369→44.717 Å / SU ML: 0.62 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.369→44.717 Å
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Refine LS restraints |
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LS refinement shell |
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