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Yorodumi- PDB-4eyk: Crystal structure of solute binding protein of ABC transporter fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4eyk | ||||||
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Title | Crystal structure of solute binding protein of ABC transporter from Rhodopseudomonas palustris BisB5 in complex with 3,4-dihydroxy benzoic acid | ||||||
Components | Twin-arginine translocation pathway signal | ||||||
Keywords | TRANSPORT PROTEIN / PSI-BIOLOGY / MCSG / MIDWEST CENTER FOR STRUCTURAL GENOMICS / transporter / lignin degradation product | ||||||
Function / homology | Function and homology information Leucine-binding protein domain / Periplasmic binding protein / Response regulator / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Chang, C. / Mack, J. / Zerbs, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Characterization of transport proteins for aromatic compounds derived from lignin: benzoate derivative binding proteins. Authors: Michalska, K. / Chang, C. / Mack, J.C. / Zerbs, S. / Joachimiak, A. / Collart, F.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4eyk.cif.gz | 163.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4eyk.ent.gz | 136.1 KB | Display | PDB format |
PDBx/mmJSON format | 4eyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/4eyk ftp://data.pdbj.org/pub/pdb/validation_reports/ey/4eyk | HTTPS FTP |
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-Related structure data
Related structure data | 4evqC 4evrC 4evsC 4ey3C 4eygC 4f06C C: citing same article (ref.) |
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Similar structure data | |
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: 39983.023 Da / Num. of mol.: 1 / Fragment: UNP residues 27-392 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Strain: BisB5 / Gene: RPD_1586 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q13AR6 |
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#2: Chemical | ChemComp-DHB / |
#3: Chemical | ChemComp-EDO / |
#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: 2.5 Å3/Da / Density % sol: 50.79 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1M SODIUM CITRATE, 20% ISO-PROPANOL,20% PEG 4000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2011 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 31877 / Num. obs: 31855 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 38.2 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 3.27 / Num. unique all: 1595 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.987 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.292 / ESU R Free: 0.113 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.51 Å2 / Biso mean: 37.0376 Å2 / Biso min: 19.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.904→1.953 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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