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Yorodumi- PDB-4z3g: Crystal structure of the lectin domain of PapG from E. coli BI47 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z3g | |||||||||
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Title | Crystal structure of the lectin domain of PapG from E. coli BI47 in complex with 4-methoxyphenyl beta-D-galabiose in space group P212121 | |||||||||
Components | PapG, lectin domain | |||||||||
Keywords | SUGAR BINDING PROTEIN / UPEC / urinary tract infection / fimbrial adhesin / adhesin / type I pili / PapG / carbohydrate binding | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | |||||||||
Authors | Jakob, R.P. / Navarra, G. / Zihlmann, P. / Stangier, K. / Preston, R.C. / Rabbani, S. / Maier, T. / Ernst, B. | |||||||||
Citation | Journal: To Be Published Title: An unexpected way nature improves solvation entropy Authors: Navarra, G. / Zihlmann, P. / Jakob, R.P. / Stangier, K. / Preston, R.C. / Rabbani, S. / Maier, T. / Ernst, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z3g.cif.gz | 332.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z3g.ent.gz | 271.2 KB | Display | PDB format |
PDBx/mmJSON format | 4z3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/4z3g ftp://data.pdbj.org/pub/pdb/validation_reports/z3/4z3g | HTTPS FTP |
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-Related structure data
Related structure data | 4z3fC 4z3hC 4z3iC 4z3jC 1j8sS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22755.660 Da / Num. of mol.: 2 / Fragment: residues 20-216 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 4-5674999 / Gene: G801_04654, G801_04690 / Plasmid: pET-22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ADA494 / References: UniProt: T7DCJ2, UniProt: A0A182DW20*PLUS #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.23 % / Description: plate like |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / Details: 10 % PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97618 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97618 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→57.66 Å / Num. obs: 69025 / % possible obs: 99.2 % / Redundancy: 11.5 % / Biso Wilson estimate: 22.46 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 1.45→1.5 Å / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.3 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1j8s Resolution: 1.45→57.66 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.9625 / SU R Cruickshank DPI: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.069 / SU Rfree Blow DPI: 0.067 / SU Rfree Cruickshank DPI: 0.065
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Displacement parameters | Biso mean: 24.23 Å2
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Refine analyze | Luzzati coordinate error obs: 0.189 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.45→57.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.49 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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