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Yorodumi- PDB-6qgy: Crystal structure of E.coli BamA beta-barrel in complex with nano... -
+Open data
-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 | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Beta-Barrel / outer membrane / protein insertion / protein folding / protein maturation | ||||||
Function / homology | Function and homology information Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane Similarity search - Function | ||||||
Biological species | Escherichia coli O157:H7 (bacteria) Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.509 Å | ||||||
Authors | Hartmann, J.-B. / Kaur, H. / Jakob, R.P. / Zahn, M. / Zimmermann, I. / Seeger, M. / Maier, T. / Hiller, S. | ||||||
Citation | Journal: J.Biomol.Nmr / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qgy.cif.gz | 373.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qgy.ent.gz | 308 KB | Display | PDB format |
PDBx/mmJSON format | 6qgy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qgy_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 6qgy_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 6qgy_validation.xml.gz | 38.6 KB | Display | |
Data in CIF | 6qgy_validation.cif.gz | 53.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/6qgy ftp://data.pdbj.org/pub/pdb/validation_reports/qg/6qgy | HTTPS FTP |
-Related structure data
Related structure data | 6qgwC 6qgxC 4n75S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Escherichia coli O157:H7 (bacteria) / Gene: bamA, yaeT, Z0188, ECs0179 / Plasmid: pET15a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A942 #2: Antibody | Mass: 13637.087 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria) #3: Chemical | ChemComp-C8E / ( #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998 Å |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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