+Open data
-Basic information
Entry | Database: PDB / ID: 5or1 | ||||||
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Title | BamA structure of Salmonella enterica | ||||||
Components | Outer membrane protein assembly factor BamA | ||||||
Keywords | MEMBRANE PROTEIN / Outer membrane protein | ||||||
Function / homology | Function and homology information Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å | ||||||
Authors | Dong, C. / Gu, Y. | ||||||
Citation | Journal: Biochem. J. / Year: 2017 Title: BamA beta 16C strand and periplasmic turns are critical for outer membrane protein insertion and assembly. Authors: Gu, Y. / Zeng, Y. / Wang, Z. / Dong, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5or1.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5or1.ent.gz | 68.1 KB | Display | PDB format |
PDBx/mmJSON format | 5or1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/5or1 ftp://data.pdbj.org/pub/pdb/validation_reports/or/5or1 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 89617.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Gene: bamA, yaeT, STM0224 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8ZRP0 |
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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: 3.49 Å3/Da / Density % sol: 64.76 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES sodium (pH 7.5) and 1.0 M sodium citrate tribasic dehydrate |
-Data collection
Diffraction | Mean temperature: 146 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.92→130 Å / Num. obs: 13411 / % possible obs: 100 % / Redundancy: 17.3 % / Net I/σ(I): 7.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.92→107.42 Å / Cor.coef. Fo:Fc: 0.855 / Cor.coef. Fo:Fc free: 0.874 / SU B: 20.586 / SU ML: 0.397 / Cross valid method: THROUGHOUT / ESU R: 1.524 / ESU R Free: 0.494 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.624 Å2
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Refinement step | Cycle: 1 / Resolution: 2.92→107.42 Å
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