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Yorodumi- PDB-4evq: Crystal structure of ABC transporter from R. palustris - solute b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4evq | ||||||
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Title | Crystal structure of ABC transporter from R. palustris - solute binding protein (RPA0668) in complex with 4-hydroxybenzoate | ||||||
Components | Putative ABC transporter subunit, substrate-binding component | ||||||
Keywords | TRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / ABC transporter / solute binding protein / benzoate-derivatives binding | ||||||
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å | ||||||
Authors | Michalska, K. / Mack, J.C. / Zerbs, S. / Collart, F.R. / 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 | 4evq.cif.gz | 308.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4evq.ent.gz | 259.6 KB | Display | PDB format |
PDBx/mmJSON format | 4evq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4evq_validation.pdf.gz | 493.4 KB | Display | wwPDB validaton report |
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Full document | 4evq_full_validation.pdf.gz | 499.4 KB | Display | |
Data in XML | 4evq_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 4evq_validation.cif.gz | 51.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/4evq ftp://data.pdbj.org/pub/pdb/validation_reports/ev/4evq | HTTPS FTP |
-Related structure data
Related structure data | 4evrC 4evsC 4ey3C 4eygC 4eykC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39241.891 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Strain: CGA009 / Gene: hbaE, RPA0668 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Magic / References: UniProt: G3XCQ4 |
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-Non-polymers , 6 types, 654 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.37 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.2 M Li2SO4, 0.1 M sodium acetate/acetic acid, 30% PEG8K, 5mM sodium 4-hydroxybenzoate, pH 4.5, 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: 0.97932 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2011 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97932 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 145161 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 2.8 / Num. unique all: 7121 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.4→35.15 Å / SU ML: 0.27 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 13.97 / Stereochemistry target values: ML Details: hydrogen atoms have been added at the riding positions
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Solvent computation | Shrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.518 Å2 / ksol: 0.447 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.4→35.15 Å
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Refine LS restraints |
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LS refinement shell |
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