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Open data
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Basic information
Entry | Database: PDB / ID: 3q54 | ||||||
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Title | Crystal structure of Escherichia coli BamB | ||||||
![]() | Outer membrane assembly lipoprotein YfgL | ||||||
![]() | LIPID BINDING PROTEIN / Lipoprotein / BamB | ||||||
Function / homology | : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dong, C. / Hou, H. / Yang, X. | ||||||
![]() | ![]() Title: Structure of Escherichia coli BamB and its interaction with POTRA domains of BamA. Authors: Dong, C. / Yang, X. / Hou, H.F. / Shen, Y.Q. / Dong, Y.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.8 KB | Display | ![]() |
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PDB format | ![]() | 124.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.1 KB | Display | ![]() |
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Full document | ![]() | 428.3 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 27.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 39317.723 Da / Num. of mol.: 1 / Fragment: UNP residues 25-392 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Lithium sulfate monohydrate 0.1M BIS-TRIS, pH 6.5, 25%PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 30, 2009 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2→89 Å / Num. all: 25190 / % possible obs: 78.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 60.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.775 Å2 / ksol: 0.351 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.004→29.196 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 10.7261 Å / Origin y: 39.0286 Å / Origin z: 45.0395 Å
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Refinement TLS group | Selection details: all |