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- PDB-8azb: Crystal Structure of the peptide binding protein DppE from Bacill... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8azb | ||||||
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Title | Crystal Structure of the peptide binding protein DppE from Bacillus subtilis in the unliganded state | ||||||
![]() | Dipeptide-binding protein DppE | ||||||
![]() | TRANSPORT PROTEIN / Peptide-binding protein / murein tripeptide / Bacillus subtilis | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hughes, A.M. / Dodson, E.J. / Wilkinson, A.J. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 219.5 KB | Display | ![]() |
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PDB format | ![]() | 168 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419.3 KB | Display | ![]() |
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Full document | ![]() | 421.8 KB | Display | |
Data in XML | ![]() | 24.2 KB | Display | |
Data in CIF | ![]() | 37.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8areC ![]() 8arnC ![]() 8ay0SC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 59501.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: dppE, dciAE, BSU12960 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.78 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: Ligand free DppE was crystallised in a sitting drop formed by mixing 150 nl of the unliganded protein at 9 mg.ml-1 with 150 nl of 0.1 M MIB buffer pH 4.0, 25 % (w/v) PEG 1500. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2016 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.4→46.09 Å / Num. obs: 104801 / % possible obs: 99.6 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.026 / Rrim(I) all: 0.053 / Net I/σ(I): 20.9 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8AY0 Resolution: 1.4→46.089 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.994 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.064 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: 16.093 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→46.089 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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