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Yorodumi- PDB-3ukj: Crystal structure of extracellular ligand-binding receptor from R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ukj | |||||||||
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Title | Crystal structure of extracellular ligand-binding receptor from Rhodopseudomonas palustris HaA2 | |||||||||
Components | Extracellular ligand-binding receptor | |||||||||
Keywords | TRANSPORT PROTEIN / PSI-BIOLOGY / MCSG / MIDWEST CENTER FOR STRUCTURAL GENOMICS / transporter | |||||||||
Function / homology | Function and homology information Leucine-binding protein domain / Periplasmic binding protein / Response regulator / 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: 1.6 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 | 3ukj.cif.gz | 164.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ukj.ent.gz | 136.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ukj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/3ukj ftp://data.pdbj.org/pub/pdb/validation_reports/uk/3ukj | HTTPS FTP |
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-Related structure data
Related structure data | 3rpwC 3sg0C 3tx6C 3uk0C 4dqdC 4eyoC 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
#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 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q2IU40 |
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#2: Chemical | ChemComp-ENO / |
#3: Chemical | ChemComp-PR / |
#4: Chemical | ChemComp-GOL / |
#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 Å3/Da / Density % sol: 38.63 % |
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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: 0.97921 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 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: 1.6→50 Å / Num. all: 42597 / Num. obs: 42082 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 31.9 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.46 / Num. unique all: 2037 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.724 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.095 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.06 Å2 / Biso mean: 18.1433 Å2 / Biso min: 6.56 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.595→1.636 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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