+Open data
-Basic information
Entry | Database: PDB / ID: 2axc | ||||||
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Title | Crystal structure of ColE7 translocation domain | ||||||
Components | Colicin E7 | ||||||
Keywords | HYDROLASE / colicin / translocation domain | ||||||
Function / homology | Function and homology information extrachromosomal circular DNA / endonuclease activity / killing of cells of another organism / Hydrolases; Acting on ester bonds / defense response to bacterium / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli str. K12 substr. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Cheng, Y.S. / Shi, Z. / Doudeva, L.G. / Yang, W.Z. / Chak, K.F. / Yuan, H.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: High-resolution crystal structure of a truncated ColE7 translocation domain: implications for colicin transport across membranes Authors: Cheng, Y.S. / Shi, Z. / Doudeva, L.G. / Yang, W.Z. / Chak, K.F. / Yuan, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2axc.cif.gz | 60.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2axc.ent.gz | 46.9 KB | Display | PDB format |
PDBx/mmJSON format | 2axc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/2axc ftp://data.pdbj.org/pub/pdb/validation_reports/ax/2axc | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 27587.424 Da / Num. of mol.: 1 / Fragment: N-terminal Translocation domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli str. K12 substr. (bacteria) Species: Escherichia coli / Strain: W3110 / Gene: colE7 (AMINO ACIDS 60-316) / Plasmid: pQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): BL834 (DE3) References: UniProt: Q47112, Hydrolases; Acting on ester bonds |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-GOL / |
#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: 2.34 Å3/Da / Density % sol: 47.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris-HCl pH 8.5, 1.5M (NH4)2SO4, 12% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 120 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9795, 0.9797, 0.9805 | ||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 7, 2004 / Details: mirrors | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→40 Å / Num. all: 313569 / Num. obs: 29942 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 20.9 Å2 / Rsym value: 0.07 / Net I/σ(I): 68.5 | ||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Mean I/σ(I) obs: 12.2 / Num. unique all: 2956 / Rsym value: 0.248 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→29.52 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 890287.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.6241 Å2 / ksol: 0.398533 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→29.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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