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Yorodumi- PDB-3t51: Crystal structures of the pre-extrusion and extrusion states of t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t51 | ||||||
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Title | Crystal structures of the pre-extrusion and extrusion states of the CusBA adaptor-transporter complex | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / transmembrane helix / heavy metal efflux | ||||||
Function / homology | Function and homology information silver ion transport / silver ion transmembrane transporter activity / plasma membrane copper ion transport / copper ion transmembrane transport / response to silver ion / silver ion transmembrane transport / cell envelope / copper ion export / copper ion transmembrane transporter activity / detoxification of copper ion ...silver ion transport / silver ion transmembrane transporter activity / plasma membrane copper ion transport / copper ion transmembrane transport / response to silver ion / silver ion transmembrane transport / cell envelope / copper ion export / copper ion transmembrane transporter activity / detoxification of copper ion / response to copper ion / xenobiotic transmembrane transporter activity / intracellular copper ion homeostasis / transition metal ion binding / response to toxic substance / outer membrane-bounded periplasmic space / copper ion binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement_SAD / Resolution: 3.9 Å | ||||||
Authors | Su, C.-C. / Long, F. / Yu, E.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Charged Amino Acids (R83, E567, D617, E625, R669, and K678) of CusA Are Required for Metal Ion Transport in the Cus Efflux System. Authors: Su, C.C. / Long, F. / Lei, H.T. / Bolla, J.R. / Do, S.V. / Rajashankar, K.R. / Yu, E.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t51.cif.gz | 629.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t51.ent.gz | 521.4 KB | Display | PDB format |
PDBx/mmJSON format | 3t51.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/3t51 ftp://data.pdbj.org/pub/pdb/validation_reports/t5/3t51 | HTTPS FTP |
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-Related structure data
-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
#1: Protein | Mass: 36615.660 Da / Num. of mol.: 2 / Fragment: UNP residues 78-407 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0574, cusB, JW0563, ylcD / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P77239 #2: Protein | | Mass: 115702.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0575, cusA, cusB, JW0564, ybdE / Production host: Escherichia coli (E. coli) / References: UniProt: P38054 #3: Chemical | |
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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: 4.41 Å3/Da / Density % sol: 72.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 Details: 10% PEG3350, 0.4M NH4SO4, 10% Glycerol, pH 7.0, vapor diffusion, temperature 298K, VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9798 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 3.9→50 Å / Num. obs: 28809 / % possible obs: 93.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 3.9→4 Å / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement_SAD / Resolution: 3.9→50 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.53 / σ(F): 0 / Phase error: 30.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 125.936 Å2 / ksol: 0.335 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 551.48 Å2 / Biso mean: 139.144 Å2 / Biso min: 32.93 Å2
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Refinement step | Cycle: LAST / Resolution: 3.9→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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