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Open data
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Basic information
Entry | Database: PDB / ID: 2yhc | ||||||
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Title | Structure of BamD from E. coli | ||||||
![]() | UPF0169 LIPOPROTEIN YFIO | ||||||
![]() | MEMBRANE PROTEIN / LIPOPROTEIN / ESSENTIAL BAM COMPONENT | ||||||
Function / homology | ![]() Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zeth, K. / Albrecht, R. | ||||||
![]() | ![]() Title: Structural Basis of Outer Membrane Protein Biogenesis in Bacteria. Authors: Albrecht, R. / Zeth, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.5 KB | Display | ![]() |
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PDB format | ![]() | 77.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.9 KB | Display | ![]() |
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Full document | ![]() | 446 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 25959.949 Da / Num. of mol.: 1 / Fragment: RESIDUES 29-245 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-URE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.14 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 30% PEG 4000, 10% I-PROH, 0.1 M HEPES PH 7.5 . |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 16896 / % possible obs: 99.4 % / Observed criterion σ(I): 3.9 / Redundancy: 6.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.9 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.8→28.39 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.041 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.667 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→28.39 Å
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Refine LS restraints |
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