+Open data
-Basic information
Entry | Database: PDB / ID: 5dl5 | ||||||
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Title | Crystal structure of Acinetobacter baumannii OccAB1 | ||||||
Components | Membrane protein | ||||||
Keywords | MEMBRANE PROTEIN / outer membrane protein / beta-barrel / antibiotic uptake | ||||||
Function / homology | Porin / Porin / Beta Barrel / Mainly Beta / PHOSPHATE ION / : Function and homology information | ||||||
Biological species | Acinetobacter baumannii AB307-0294 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Zahn, M. / Basle, A. / van den Berg, B. | ||||||
Citation | Journal: Structure / Year: 2016 Title: Structural Insights into Outer Membrane Permeability of Acinetobacter baumannii. Authors: Zahn, M. / Bhamidimarri, S.P. / Basle, A. / Winterhalter, M. / van den Berg, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dl5.cif.gz | 178.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dl5.ent.gz | 140.6 KB | Display | PDB format |
PDBx/mmJSON format | 5dl5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/5dl5 ftp://data.pdbj.org/pub/pdb/validation_reports/dl/5dl5 | HTTPS FTP |
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-Related structure data
Related structure data | 5dl6C 5dl7C 5dl8C 3sysS 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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Unit cell |
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-Components
#1: Protein | Mass: 47476.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii AB307-0294 (bacteria) Gene: VM83_01045 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F5EN03 | ||||
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#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.63 % |
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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 sulphate, 0.1 M sodium citrate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→116.11 Å / Num. obs: 35036 / % possible obs: 99.2 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.05→2.11 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.1 / % possible all: 96 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SYS Resolution: 2.05→116.11 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.63 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.146 / 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: 42.53 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→116.11 Å
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Refine LS restraints |
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