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Yorodumi- PDB-3rpw: The crystal structure of an ABC transporter from Rhodopseudomonas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rpw | ||||||
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Title | The crystal structure of an ABC transporter from Rhodopseudomonas palustris CGA009 | ||||||
Components | ABC transporterATP-binding cassette transporter | ||||||
Keywords | TRANSPORT PROTEIN / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å | ||||||
Authors | Tan, K. / Mack, J.C. / 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 | 3rpw.cif.gz | 152.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rpw.ent.gz | 126.9 KB | Display | PDB format |
PDBx/mmJSON format | 3rpw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/3rpw ftp://data.pdbj.org/pub/pdb/validation_reports/rp/3rpw | HTTPS FTP |
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-Related structure data
Related structure data | 3sg0C 3tx6C 3uk0C 3ukjC 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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Details | Experimentally unknown. It is predicted that the molecule is monomeric. |
-Components
#1: Protein | Mass: 40730.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Strain: CGA009 / Gene: RPA4648 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q6N0W2 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-URE / | #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: 2.53 Å3/Da / Density % sol: 51.41 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.4M Sodium Malonate, pH 7.0, 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-BM / Wavelength: 0.97923 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2011 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→32.5 Å / Num. all: 50234 / Num. obs: 50234 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 36.3 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2531 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.65→32.5 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 17.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.898 Å2 / ksol: 0.438 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.65→32.5 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 3.0055 Å / Origin y: 50.4873 Å / Origin z: 20.4975 Å
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Refinement TLS group | Selection details: all |