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Yorodumi- PDB-4z3e: Crystal structure of the lectin domain of PapG from E. coli BI47 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z3e | |||||||||
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Title | Crystal structure of the lectin domain of PapG from E. coli BI47 in complex with SSEA4 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: 1.8 Å | |||||||||
Authors | Jakob, R.P. / Navarra, G. / Zihlmann, P. / Stangier, K. / Preston, R.C. / Rabbani, S. / Maier, T. / Ernst, B. | |||||||||
Citation | Journal: Chembiochem / Year: 2017 Title: Carbohydrate-Lectin Interactions: An Unexpected Contribution to Affinity. Authors: Navarra, G. / Zihlmann, P. / Jakob, R.P. / Stangier, K. / Preston, R.C. / Rabbani, S. / Smiesko, M. / Wagner, B. / 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 | 4z3e.cif.gz | 103.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z3e.ent.gz | 78.2 KB | Display | PDB format |
PDBx/mmJSON format | 4z3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z3e_validation.pdf.gz | 812 KB | Display | wwPDB validaton report |
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Full document | 4z3e_full_validation.pdf.gz | 815.1 KB | Display | |
Data in XML | 4z3e_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 4z3e_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/4z3e ftp://data.pdbj.org/pub/pdb/validation_reports/z3/4z3e | HTTPS FTP |
-Related structure data
Related structure data | 4z3fC 4z3gC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22755.660 Da / Num. of mol.: 1 / Fragment: residues 20-216 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: pET-22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ADA494 / References: UniProt: T7DCJ2, UniProt: A0A182DW20*PLUS |
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#2: Polysaccharide | beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.55 % / Description: plate |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.15M ZnAcetate, 0.05M ZnCl2, 0.1MTris pH 7.5, 13% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→43.1 Å / Num. obs: 17523 / % possible obs: 99.9 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.5 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1j8s Resolution: 1.8→43.1 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.971 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.136 / 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: 28.14 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→43.1 Å
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