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- PDB-4dqd: The crystal structure of a transporter in complex with 3-phenylpy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dqd | ||||||
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Title | The crystal structure of a transporter in complex with 3-phenylpyruvic acid | ||||||
![]() | Extracellular ligand-binding receptor | ||||||
![]() | SIGNALING PROTEIN / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural ge nomics / MCSG / Midwest Center for Structural Genomics | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tan, K. / Mack, J.C. / Zerbs, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.5 KB | Display | ![]() |
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PDB format | ![]() | 124.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3rpwC ![]() 3sg0SC ![]() 3tx6C ![]() 3uk0C ![]() 3ukjC ![]() 4eyoC ![]() 4eyqC ![]() 4f8jC ![]() 4fb4C ![]() 4i1dC S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | Experimentally unknown. It is predicted to be monomeric. |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38942.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: HaA2 / Gene: RPB_4630 / References: UniProt: Q2IR47 |
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-Non-polymers , 5 types, 346 molecules ![](data/chem/img/PPY.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/3PY.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/3PY.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PPY / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-3PY / | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.79 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Trimethylamine N-oxide, 0.1M Tris:HCl, 20% (w/v) PEG MME 2000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2012 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→26 Å / Num. all: 56211 / Num. obs: 56211 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.6→1.62 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2210 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 3SG0 Resolution: 1.601→25.97 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 15.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.379 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.601→25.97 Å
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Refine LS restraints |
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LS refinement shell |
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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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