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Yorodumi- PDB-4qfl: Crystal structure of dipeptide binding protein from pseudoalterom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qfl | ||||||
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Title | Crystal structure of dipeptide binding protein from pseudoalteromonas sp. SM9913 in complex with Ala-Phe | ||||||
Components | ABC transporter periplasmic peptide-binding protein | ||||||
Keywords | PEPTIDE BINDING PROTEIN / dipeptide binding protein | ||||||
Function / homology | Function and homology information dipeptide transport / peptide transmembrane transporter activity / peptide transport / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | Pseudoalteromonas (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.749 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 | 4qfl.cif.gz | 226.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qfl.ent.gz | 179.9 KB | Display | PDB format |
PDBx/mmJSON format | 4qfl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qfl_validation.pdf.gz | 485 KB | Display | wwPDB validaton report |
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Full document | 4qfl_full_validation.pdf.gz | 506.2 KB | Display | |
Data in XML | 4qfl_validation.xml.gz | 45.9 KB | Display | |
Data in CIF | 4qfl_validation.cif.gz | 67 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/4qfl ftp://data.pdbj.org/pub/pdb/validation_reports/qf/4qfl | HTTPS FTP |
-Related structure data
Related structure data | 4qfkC 4qfnC 4qfoC 4qfpC 1dppS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 61762.934 Da / Num. of mol.: 2 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: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.66 Å3/Da / Density % sol: 53.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.5M sodium phosphate monobasic monohydrate, 0.9M potassium phosphate dibasic, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: May 10, 2013 |
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: 1.749→50 Å / Num. all: 126524 / Num. obs: 126524 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.1 Å2 |
Reflection shell | Resolution: 1.75→1.81 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1dpp Resolution: 1.749→33.988 Å / FOM work R set: 0.7761 / σ(F): 0 / Phase error: 30.18 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.217 Å2 / ksol: 0.35 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.47 Å2 / Biso mean: 24.45 Å2 / Biso min: 12.41 Å2
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Refinement step | Cycle: LAST / Resolution: 1.749→33.988 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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