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Yorodumi- PDB-4evs: Crystal structure of ABC transporter from R. palustris - solute b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4evs | ||||||
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Title | Crystal structure of ABC transporter from R. palustris - solute binding protein (RPA0985) 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 | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 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 | 4evs.cif.gz | 162.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4evs.ent.gz | 134.7 KB | Display | PDB format |
PDBx/mmJSON format | 4evs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/4evs ftp://data.pdbj.org/pub/pdb/validation_reports/ev/4evs | HTTPS FTP |
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-Related structure data
Related structure data | 4evqC 4evrC 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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Unit cell |
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-Components
#1: Protein | Mass: 40400.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Strain: CGA009 / Gene: RPA0985 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Magic / References: UniProt: Q6NB45 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-PHB / | #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: 2.03 Å3/Da / Density % sol: 39.33 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: 2 M (NH4)2SO4, 0.1 M citric acid/NaOH , pH 3.5, 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: 0.97935 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2011 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. all: 59525 / Num. obs: 59333 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2906 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.45→39.78 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.333 / SU ML: 0.04 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGEN ATOMS HAVE BEEN ADDED AT THE RIDING POSITIONS
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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 mean: 16.86 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→39.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.447→1.485 Å / Total num. of bins used: 20
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