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Yorodumi- PDB-4dz1: Crystal structure of DalS, an ATP binding cassette transporter fo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dz1 | ||||||
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Title | Crystal structure of DalS, an ATP binding cassette transporter for D-alanine from Salmonella enterica | ||||||
Components | DalS D-Alanine transporter | ||||||
Keywords | TRANSPORT PROTEIN / D-alanine binding / periplasmic | ||||||
Function / homology | Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / D-ALANINE / : Function and homology information | ||||||
Biological species | Salmonella enterica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Mok, M. / Junop, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Characterization of DalS, an ATP-binding Cassette Transporter for D-Alanine, and Its Role in Pathogenesis in Salmonella enterica. Authors: Osborne, S.E. / Tuinema, B.R. / Mok, M.C. / Lau, P.S. / Bui, N.K. / Tomljenovic-Berube, A.M. / Vollmer, W. / Zhang, K. / Junop, M. / Coombes, B.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dz1.cif.gz | 103.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dz1.ent.gz | 84.4 KB | Display | PDB format |
PDBx/mmJSON format | 4dz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dz1_validation.pdf.gz | 439.7 KB | Display | wwPDB validaton report |
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Full document | 4dz1_full_validation.pdf.gz | 440.7 KB | Display | |
Data in XML | 4dz1_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 4dz1_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/4dz1 ftp://data.pdbj.org/pub/pdb/validation_reports/dz/4dz1 | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 29769.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: LTSEBAI_2502 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: G9W5C4 |
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#2: Chemical | ChemComp-DAL / |
#3: 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: 2.99 Å3/Da / Density % sol: 58.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 10% w/v PEG3000, 0.1 M sodium/potassium phosphate, pH 6.2, 5 mM glycine, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2011 Details: vertically focusing mirror, horizontally focusing monochromator |
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 28940 / Num. obs: 28940 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 21 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 21 % / Rmerge(I) obs: 0.839 / Mean I/σ(I) obs: 4.7 / Num. unique all: 2761 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→39.047 Å / SU ML: 0.21 / σ(F): 0.3 / Phase error: 18.22 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.779 Å2 / ksol: 0.34 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→39.047 Å
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Refine LS restraints |
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LS refinement shell |
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