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Open data
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Basic information
Entry | Database: PDB / ID: 5ekq | |||||||||
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Title | The structure of the BamACDE subcomplex from E. coli | |||||||||
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![]() | MEMBRANE PROTEIN / insertase / beta-barrel / outer membrane protein | |||||||||
Function / homology | ![]() Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / protein-macromolecule adaptor activity / cell adhesion / response to antibiotic / cell surface / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Bakelar, J. / Buchanan, S.K. / Noinaj, N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The structure of the beta-barrel assembly machinery complex. Authors: Bakelar, J. / Buchanan, S.K. / Noinaj, N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 257.5 KB | Display | ![]() |
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PDB format | ![]() | 198.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.8 KB | Display | ![]() |
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Full document | ![]() | 494.2 KB | Display | |
Data in XML | ![]() | 45.7 KB | Display | |
Data in CIF | ![]() | 61.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2km7S ![]() 3efcS ![]() 3q6bS ![]() 3tgoS ![]() 4c4vS S: Starting model for refinement |
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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
#1: Protein | Mass: 88514.742 Da / Num. of mol.: 1 / Fragment: UNP residues 21-810 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: bamA, yaeT, yzzN, yzzY, b0177, JW0172 / Production host: ![]() ![]() |
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#2: Protein | Mass: 25816.818 Da / Num. of mol.: 1 / Fragment: UNP residues 20-245 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: bamD, yfiO, b2595, JW2577 / Production host: ![]() ![]() |
#3: Protein | Mass: 34401.250 Da / Num. of mol.: 1 / Fragment: UNP residues 25-344 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: bamC, dapX, nlpB, b2477, JW2462 / Production host: ![]() ![]() |
#4: Protein | Mass: 10391.554 Da / Num. of mol.: 1 / Fragment: UNP residues 20-113 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: bamE, smpA, b2617, JW2598 / Production host: ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.17 Å3/Da / Density % sol: 70.54 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM Tris-HCl, pH 8.5, 200 mM MgCl2, 10 mM MnCl2, and 8% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Aug 19, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.392→50 Å / Num. obs: 36099 / % possible obs: 99.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 133.43 Å2 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.058 / Rrim(I) all: 0.129 / Χ2: 1.596 / Net I/av σ(I): 21.346 / Net I/σ(I): 5.8 / Num. measured all: 226289 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB IDs 3TGO 4C4V 3Q6B 2KM7 3EFC Resolution: 3.392→29.914 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.07 / 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: 3.392→29.914 Å
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Refine LS restraints |
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LS refinement shell |
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