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Yorodumi- PDB-6fsu: Crystal structure of E.coli BamA beta-barrel with a C-terminal ex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fsu | ||||||
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Title | Crystal structure of E.coli BamA beta-barrel with a C-terminal extension | ||||||
Components | Outer membrane protein assembly factor BamA | ||||||
Keywords | MEMBRANE PROTEIN | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Zahn, M. / Hartmann, J.-B. / Hiller, S. | ||||||
Citation | Journal: J. Am. Chem. Soc. / Year: 2018 Title: Sequence-Specific Solution NMR Assignments of the beta-Barrel Insertase BamA to Monitor Its Conformational Ensemble at the Atomic Level. Authors: Hartmann, J.B. / Zahn, M. / Burmann, I.M. / Bibow, S. / Hiller, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fsu.cif.gz | 316.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fsu.ent.gz | 259 KB | Display | PDB format |
PDBx/mmJSON format | 6fsu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fsu_validation.pdf.gz | 444.7 KB | Display | wwPDB validaton report |
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Full document | 6fsu_full_validation.pdf.gz | 457.2 KB | Display | |
Data in XML | 6fsu_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 6fsu_validation.cif.gz | 39.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/6fsu ftp://data.pdbj.org/pub/pdb/validation_reports/fs/6fsu | HTTPS FTP |
-Related structure data
Related structure data | 4n75S S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 412 - 819 / Label seq-ID: 13 - 420
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-Components
#1: Protein | Mass: 47029.902 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A942 #2: 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: 2.91 Å3/Da / Density % sol: 57.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 22 % (w/v) PEG 400, 0.07 M NaCl, 0.05 M sodium citrate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→66.84 Å / Num. obs: 34607 / % possible obs: 99.8 % / Redundancy: 5.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.111 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.072 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4151 / CC1/2: 0.647 / Rpim(I) all: 0.768 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4N75 Resolution: 2.6→66.84 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.903 / SU B: 35.924 / SU ML: 0.335 / Cross valid method: THROUGHOUT / ESU R: 0.626 / ESU R Free: 0.343 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.603 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→66.84 Å
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Refine LS restraints |
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