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Yorodumi- PDB-4f3s: Crystal structure of periplasmic D-alanine ABC transporter from S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f3s | |||||||||
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Title | Crystal structure of periplasmic D-alanine ABC transporter from Salmonella enterica | |||||||||
Components | Putative periplasmic binding protein | |||||||||
Keywords | TRANSPORT PROTEIN / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / periplasmic | |||||||||
Function / homology | Function and homology information Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | |||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14 Å | |||||||||
Authors | Agarwal, R. / Chamala, S. / Evans, B. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Siedel, R. / Villigas, G. / Zencheck, W. ...Agarwal, R. / Chamala, S. / Evans, B. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Siedel, R. / Villigas, G. / Zencheck, W. / Foti, R. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC) | |||||||||
Citation | Journal: To be Published Title: Crystal structure of periplasmic D-alanine ABC transporter from Salmonella enterica Authors: Agarwal, R. / Almo, S.C. / Swaminathan, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f3s.cif.gz | 56.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f3s.ent.gz | 44.6 KB | Display | PDB format |
PDBx/mmJSON format | 4f3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/4f3s ftp://data.pdbj.org/pub/pdb/validation_reports/f3/4f3s | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29598.467 Da / Num. of mol.: 1 / Fragment: UNP residues 23-253 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Gene: STM1633 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q8ZPA3 |
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#2: Chemical | ChemComp-GLY / |
#3: Chemical | ChemComp-DAL / |
#4: Chemical | ChemComp-PO4 / |
#5: 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: 2.95 Å3/Da / Density % sol: 58.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.8M Ammonium citrate tribasic pH 7, 10% Jeffamine M600 pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2011 / Details: Mirrors |
Radiation | Monochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→50 Å / Num. all: 20516 / Num. obs: 20516 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 41 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.14→2.22 Å / Redundancy: 37.83 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 5 / Num. unique all: 2004 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.14→46.45 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.706 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.165 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.385 Å2
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Refinement step | Cycle: LAST / Resolution: 2.14→46.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.141→2.197 Å / Total num. of bins used: 20
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