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Yorodumi- PDB-8ay0: Crystal Structure of the peptide binding protein DppE from Bacill... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ay0 | ||||||
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Title | Crystal Structure of the peptide binding protein DppE from Bacillus subtilis in complex with murein tripeptide | ||||||
Components | Dipeptide-binding protein DppE | ||||||
Keywords | TRANSPORT PROTEIN / Peptide-binding protein / murein tripeptide / Bacillus subtilis | ||||||
Function / homology | Function and homology information peptide transport / peptide transmembrane transporter activity / sporulation resulting in formation of a cellular spore / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / protein transport / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Hughes, A.M. / Dodson, E.J. / Wilkinson, A.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Microbiology (Reading, Engl.) / Year: 2022 Title: Peptide transport in Bacillus subtilis - structure and specificity in the extracellular solute binding proteins OppA and DppE. Authors: Hughes, A.M. / Darby, J.F. / Dodson, E.J. / Wilson, S.J. / Turkenburg, J.P. / Thomas, G.H. / Wilkinson, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ay0.cif.gz | 610.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ay0.ent.gz | 487.8 KB | Display | PDB format |
PDBx/mmJSON format | 8ay0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/8ay0 ftp://data.pdbj.org/pub/pdb/validation_reports/ay/8ay0 | HTTPS FTP |
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-Related structure data
Related structure data | 8areC 8arnC 8azbC 4fajS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 59501.270 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: dppE, dciAE, BSU12960 / Production host: Escherichia coli (E. coli) / References: UniProt: P26906 #2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.23 Å3/Da / Density % sol: 44.86 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Crystals of DppE suitable for X-ray analysis were obtained from hanging drops formed by mixing 1 mircol of reservoir solution containing 0.1 M Bis-Tris-Propane pH 8.5, 0.4 M MgCl2, 22.5 % ...Details: Crystals of DppE suitable for X-ray analysis were obtained from hanging drops formed by mixing 1 mircol of reservoir solution containing 0.1 M Bis-Tris-Propane pH 8.5, 0.4 M MgCl2, 22.5 % PEG 3350 and 2.5 % DMSO with 1 microl of protein at 13 mg.ml-1 . |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2015 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.51→60.74 Å / Num. obs: 233391 / % possible obs: 96.3 % / Redundancy: 2.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.053 / Rrim(I) all: 0.075 / Net I/σ(I): 8.4 | ||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 2.2 %
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FAJ Resolution: 1.51→60.739 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.305 / SU ML: 0.079 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.084 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.662 Å2
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Refinement step | Cycle: LAST / Resolution: 1.51→60.739 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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