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Yorodumi- PDB-4pev: Crystal structure of ABC transporter system solute-binding protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pev | ||||||
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Title | Crystal structure of ABC transporter system solute-binding proteins from Aeropyrum pernix K1 | ||||||
Components | Membrane lipoprotein family protein | ||||||
Keywords | SOLUTE-BINDING PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / ABC transporter / solute binding protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aeropyrum pernix (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.58 Å | ||||||
Authors | Chang, C. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: to be published Title: Crystal structure of ABC transporter system solute-binding proteins from Aeropyrum pernix K1 Authors: Chang, C. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pev.cif.gz | 225.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pev.ent.gz | 180 KB | Display | PDB format |
PDBx/mmJSON format | 4pev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pev_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 4pev_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4pev_validation.xml.gz | 38 KB | Display | |
Data in CIF | 4pev_validation.cif.gz | 52.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/4pev ftp://data.pdbj.org/pub/pdb/validation_reports/pe/4pev | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 46082.266 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Gene: APE_2592.1 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q9Y8P1 #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: 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: 2.56 Å3/Da / Density % sol: 51.97 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.1M phosphate-citrate 1.6M Sodium phospahte/0.4M potassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97907 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.58→50 Å / Num. obs: 44392 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.195 / Χ2: 0.912 / Net I/av σ(I): 5.982 / Net I/σ(I): 4.1 / Num. measured all: 239835 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.58→49.77 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.904 / SU B: 10.111 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.328 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.36 Å2 / Biso mean: 37.613 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: final / Resolution: 2.58→49.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.583→2.65 Å / Total num. of bins used: 20
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