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Yorodumi- PDB-3drg: Lactococcal OppA complexed with bradykinin in the closed conformation -
+Open data
-Basic information
Entry | Database: PDB / ID: 3drg | ||||||
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Title | Lactococcal OppA complexed with bradykinin in the closed conformation | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / oligo-peptide binding / voluminous binding cavity / venus fly-trap | ||||||
Function / homology | Function and homology information peptide transmembrane transporter activity / peptide transport / ATP-binding cassette (ABC) transporter complex / protein transport / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | Lactococcus lactis (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Berntsson, R.P.-A. / Doeven, M.K. / Duurkens, R.H. / Sengupta, D. / Marrink, S.-J. / Thunnissen, A.-M. / Poolman, B. / Slotboom, D.-J. | ||||||
Citation | Journal: Embo J. / Year: 2009 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3drg.cif.gz | 124.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3drg.ent.gz | 94.3 KB | Display | PDB format |
PDBx/mmJSON format | 3drg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3drg_validation.pdf.gz | 435.2 KB | Display | wwPDB validaton report |
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Full document | 3drg_full_validation.pdf.gz | 436.4 KB | Display | |
Data in XML | 3drg_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 3drg_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/3drg ftp://data.pdbj.org/pub/pdb/validation_reports/dr/3drg | HTTPS FTP |
-Related structure data
Related structure data | 3drfSC 3drhC 3driC 3drjC 3drkC 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: 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.) Lactococcus lactis (lactic acid bacteria) Strain: subsp. cremoris MG1363 / Gene: oppA, llmg_0701 / Plasmid: pAMP21 / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): MG1363 / References: UniProt: A2RJ53 |
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#2: Protein/peptide | Mass: 976.108 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesis |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.38 % / Mosaicity: 0.97 ° |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC Q4 / Detector: CCD / Date: Feb 2, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 1.9 % / Av σ(I) over netI: 2 / Number: 35303 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / D res high: 2.5 Å / D res low: 58.321 Å / Num. obs: 18131 / % possible obs: 96.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.5→58.321 Å / Num. all: 35303 / Num. obs: 18131 / % possible obs: 96.2 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DRF Resolution: 2.5→58.32 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.844 / SU B: 13.901 / SU ML: 0.298 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.366 / 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: 38.656 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→58.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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