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Yorodumi- PDB-4eyo: Crystal structure of solute binding protein of ABC transporter fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4eyo | ||||||
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Title | Crystal structure of solute binding protein of ABC transporter from Rhodopseudomonas palustris HaA2 in complex with p-coumaric acid | ||||||
Components | Extracellular ligand-binding receptor | ||||||
Keywords | TRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / transporter / lignin degradation product | ||||||
Function / homology | Leucine-binding protein domain / Periplasmic binding protein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / 4'-HYDROXYCINNAMIC ACID / Extracellular ligand-binding receptor Function and homology information | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.69 Å | ||||||
Authors | Chang, C. / Mack, J. / Zerbs, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Proteins / Year: 2013 Title: Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-Coumaric acid and related aromatic acids. Authors: Tan, K. / Chang, C. / Cuff, M. / Osipiuk, J. / Landorf, E. / 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 | 4eyo.cif.gz | 160.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4eyo.ent.gz | 132.6 KB | Display | PDB format |
PDBx/mmJSON format | 4eyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/4eyo ftp://data.pdbj.org/pub/pdb/validation_reports/ey/4eyo | HTTPS FTP |
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-Related structure data
Related structure data | 3rpwC 3sg0C 3tx6C 3uk0C 3ukjC 4dqdC 4eyqC 4f8jC 4fb4C 4i1dC 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: 39194.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Strain: HaA2 / Gene: RPB_3575 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q2IU40 |
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#2: Chemical | ChemComp-HC4 / |
#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: 3.02 Å3/Da / Density % sol: 59.29 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 10 mM Nickel chloride, 0.1M Tris, 20% PEG2000 MME, 10 mM Praseodymium Acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 2, 2012 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 55110 / Num. obs: 54612 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 1.7→1.71 Å / Redundancy: 93.5 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 2.12 / Num. unique all: 1256 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.69→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.08 / SU B: 5.819 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.094 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: 93.31 Å2 / Biso mean: 29.6055 Å2 / Biso min: 13.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.69→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.691→1.735 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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