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Yorodumi- PDB-4qfk: Crystal structure of dipeptide binding protein from pseudoalterom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qfk | ||||||
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Title | Crystal structure of dipeptide binding protein from pseudoalteromonas sp. SM9913 | ||||||
Components | ABC transporter periplasmic peptide-binding protein | ||||||
Keywords | PEPTIDE BINDING PROTEIN / dipeptide binding protein | ||||||
Function / homology | Function and homology information ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | Pseudoalteromonas (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.288 Å | ||||||
Authors | Li, C.Y. / Zhang, Y.Z. | ||||||
Citation | Journal: J. Bacteriol. / Year: 2015 Title: Structural insights into the multispecific recognition of dipeptides of deep-sea gram-negative bacterium Pseudoalteromonas sp. strain SM9913 Authors: Li, C.Y. / Chen, X.L. / Qin, Q.L. / Wang, P. / Zhang, W.X. / Xie, B.B. / Su, H.N. / Zhang, X.Y. / Zhou, B.C. / Zhang, Y.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qfk.cif.gz | 816.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qfk.ent.gz | 680.1 KB | Display | PDB format |
PDBx/mmJSON format | 4qfk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/4qfk ftp://data.pdbj.org/pub/pdb/validation_reports/qf/4qfk | HTTPS FTP |
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-Related structure data
Related structure data | 4qflC 4qfnC 4qfoC 4qfpC 1dpeS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 61762.934 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoalteromonas (bacteria) / Strain: SM9913 / Gene: dppA / Production host: Escherichia coli (E. coli) / References: UniProt: A7Y7W1 #2: Water | ChemComp-HOH / | |
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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: 2.31 Å3/Da / Density % sol: 46.66 % |
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Crystal grow | Temperature: 277 K / Method: evaporation / pH: 9.2 Details: 0.2M potassium phosphate dibasic, 20%(w/v) polyethylene glycol 3350, pH 9.2, EVAPORATION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2011 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.288→50 Å / Num. all: 185390 / Num. obs: 185390 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.8 Å2 |
Reflection shell | Resolution: 2.3→2.38 Å / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1dpe Resolution: 2.288→42.629 Å / FOM work R set: 0.7975 / SU ML: 0.33 / σ(F): 0.02 / Phase error: 27.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.525 Å2 / ksol: 0.32 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.81 Å2 / Biso mean: 29.32 Å2 / Biso min: 6.91 Å2
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Refinement step | Cycle: LAST / Resolution: 2.288→42.629 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: 30
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