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- PDB-6qgy: Crystal structure of E.coli BamA beta-barrel in complex with nano... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qgy | ||||||
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Title | Crystal structure of E.coli BamA beta-barrel in complex with nanobody B12 | ||||||
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![]() | MEMBRANE PROTEIN / Beta-Barrel / outer membrane / protein insertion / protein folding / protein maturation | ||||||
Function / homology | ![]() Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hartmann, J.-B. / Kaur, H. / Jakob, R.P. / Zahn, M. / Zimmermann, I. / Seeger, M. / Maier, T. / Hiller, S. | ||||||
![]() | ![]() Title: Identification of conformation-selective nanobodies against the membrane protein insertase BamA by an integrated structural biology approach. Authors: Kaur, H. / Hartmann, J.B. / Jakob, R.P. / Zahn, M. / Zimmermann, I. / Maier, T. / Seeger, M.A. / Hiller, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 373.4 KB | Display | ![]() |
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PDB format | ![]() | 308 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6qgwC ![]() 6qgxC ![]() 4n75S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 46022.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Antibody | Mass: 13637.087 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-C8E / ( #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.37 Å3/Da / Density % sol: 71.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 32% PEG 400, 0.2 M ammonium phosphate, 0.1 M ammonium sulfate, 0.1 M sodium citrate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99998 Å / Relative weight: 1 |
Reflection | Resolution: 2.509→48.484 Å / Num. obs: 69491 / % possible obs: 98.5 % / Redundancy: 5.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.051 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.51→2.57 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3901 / CC1/2: 0.621 / Rpim(I) all: 0.699 / % possible all: 86.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4n75 Resolution: 2.509→48.484 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.64
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.509→48.484 Å
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Refine LS restraints |
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LS refinement shell |
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