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- PDB-3drj: Crystal structure of Lactococcal OppA co-crystallized with pTH-re... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3drj | ||||||
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Title | Crystal structure of Lactococcal OppA co-crystallized with pTH-related peptide in an open conformation | ||||||
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![]() | PEPTIDE BINDING PROTEIN / oligo-peptide binding / voluminous binding cavity / venus fly-trap | ||||||
Function / homology | ![]() peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / protein transport / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Berntsson, R.P.-A. / Doeven, M.K. / Duurkens, R.H. / Sengupta, D. / Marrink, S.-J. / Thunnissen, A.-M. / Poolman, B. / Slotboom, D.-J. | ||||||
![]() | ![]() Title: The structural basis for peptide selection by the transport receptor OppA Authors: Berntsson, R.P.-A. / Doeven, M.K. / Fusetti, F. / Duurkens, R.H. / Sengupta, D. / Marrink, S.-J. / Thunnissen, A.-M. / Poolman, B. / Slotboom, D.-J. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.5 KB | Display | ![]() |
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PDB format | ![]() | 109.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.4 KB | Display | ![]() |
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Full document | ![]() | 438.3 KB | Display | |
Data in XML | ![]() | 29.9 KB | Display | |
Data in CIF | ![]() | 48.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3drfSC ![]() 3drgC ![]() 3drhC ![]() 3driC ![]() 3drkC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 65144.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Construct lacking N-terminal signal sequence and cysteine used for lipid modification Source: (gene. exp.) ![]() Strain: subsp. cremoris MG1363 / Gene: oppA, llmg_0701 / Plasmid: pAMP21 / Production host: ![]() |
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#2: Protein/peptide | Mass: 498.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesis |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M NaCl, 0.1M Na-Hepes, 20% PEG 6000, pH 7.0, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC Q210 / Detector: CCD / Date: Sep 22, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→37.165 Å / Num. obs: 86038 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.434 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 17.78 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3DRF Resolution: 1.5→37.16 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.491 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.793 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→37.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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