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Yorodumi- PDB-2qcp: 1.0 A Structure of CusF-Ag(I) residues 10-88 from Escherichia coli -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qcp | ||||||
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Title | 1.0 A Structure of CusF-Ag(I) residues 10-88 from Escherichia coli | ||||||
Components | Cation efflux system protein cusF | ||||||
Keywords | METAL BINDING PROTEIN / silver-binding / copper-binding / beta barrel / OB-fold / metalloprotein / metal resistance / Metal-binding / Periplasmic | ||||||
Function / homology | Function and homology information metallochaperone activity / copper ion transmembrane transport / response to silver ion / silver ion transmembrane transport / copper chaperone activity / copper ion export / detoxification of copper ion / response to copper ion / response to zinc ion / transition metal ion binding ...metallochaperone activity / copper ion transmembrane transport / response to silver ion / silver ion transmembrane transport / copper chaperone activity / copper ion export / detoxification of copper ion / response to copper ion / response to zinc ion / transition metal ion binding / intracellular copper ion homeostasis / response to toxic substance / outer membrane-bounded periplasmic space / periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli str. K12 substr. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | ||||||
Authors | Loftin, I.R. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Unusual Cu(I)/Ag(I) coordination of Escherichia coli CusF as revealed by atomic resolution crystallography and X-ray absorption spectroscopy Authors: Loftin, I.R. / Franke, S. / Blackburn, N.J. / McEvoy, M.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qcp.cif.gz | 53.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qcp.ent.gz | 38.3 KB | Display | PDB format |
PDBx/mmJSON format | 2qcp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/2qcp ftp://data.pdbj.org/pub/pdb/validation_reports/qc/2qcp | HTTPS FTP |
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-Related structure data
Related structure data | 1zeqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8891.271 Da / Num. of mol.: 1 / Fragment: sequence database residues 32-110 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli str. K12 substr. (bacteria) Species: Escherichia coli / Strain: W3110 / Gene: cusF, cusX / Plasmid: pPR-IBA1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21-DE3 / References: UniProt: P77214 | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-AG / | #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: 1.87 Å3/Da / Density % sol: 34.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 100 mM sodium acetate trihydrate (pH 4.6), 2.3 M ammonium sulfate, 2 mM silver nitrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 29, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1→19.7 Å / Num. all: 35956 / Num. obs: 35956 / % possible obs: 97.7 % / Redundancy: 5.52 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 97.7 |
Reflection shell | Resolution: 1→1.04 Å / Redundancy: 5.09 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.1 / % possible all: 95.6 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZEQ Resolution: 1→19.68 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.819 / SU ML: 0.02 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 9.378 Å2
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Refinement step | Cycle: LAST / Resolution: 1→19.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1→1.026 Å / Total num. of bins used: 20
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