+Open data
-Basic information
Entry | Database: PDB / ID: 3zl1 | ||||||
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Title | A thiazolyl-mannoside bound to FimH, monoclinic space group | ||||||
Components | PROTEIN FIMH | ||||||
Keywords | CELL ADHESION / TYPE-1 FIMBRIAE / THIAZOLE / CROHN'S DISEASE / IMMUNOGLOBULIN | ||||||
Function / homology | Function and homology information pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / cell adhesion Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.551 Å | ||||||
Authors | Brument, S. / Sivignon, A. / Dumych, T.I. / Moreau, N. / Roos, G. / Guerardel, Y. / Chalopin, T. / Deniaud, D. / Bilyy, R.O. / Darfeuille-Michaud, A. ...Brument, S. / Sivignon, A. / Dumych, T.I. / Moreau, N. / Roos, G. / Guerardel, Y. / Chalopin, T. / Deniaud, D. / Bilyy, R.O. / Darfeuille-Michaud, A. / Bouckaert, J. / Gouin, S.G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Thiazolylaminomannosides as Potent Antiadhesives of Type 1 Piliated Escherichia Coli Isolated from Crohn'S Disease Patients. Authors: Brument, S. / Sivignon, A. / Dumych, T.I. / Moreau, N. / Roos, G. / Guerardel, Y. / Chalopin, T. / Deniaud, D. / Bilyy, R.O. / Darfeuille-Michaud, A. / Bouckaert, J. / Gouin, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zl1.cif.gz | 83.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zl1.ent.gz | 62.5 KB | Display | PDB format |
PDBx/mmJSON format | 3zl1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zl1_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 3zl1_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3zl1_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 3zl1_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/3zl1 ftp://data.pdbj.org/pub/pdb/validation_reports/zl/3zl1 | HTTPS FTP |
-Related structure data
Related structure data | 3zl2C 4auuS C: citing same article (ref.) 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9696, -0.0353, 0.242), Vector: |
-Components
#1: Protein | Mass: 16916.828 Da / Num. of mol.: 2 Fragment: LECTIN DOMAIN OR RECEPTOR BINDING DOMAIN, RESIDUES 22-179 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: J96 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: P08191 #2: Sugar | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
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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: 2.86 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.1 M NACL, 0.1 M TRIS PH 7.5, 11 % (W/V) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 |
Detector | Date: Feb 29, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→47.2 Å / Num. obs: 183542 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 10.79 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 0 |
Reflection shell | Resolution: 1.55→1.65 Å / Redundancy: 5 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.09 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AUU Resolution: 1.551→47.177 Å / SU ML: 0.18 / σ(F): 2 / Phase error: 27.94 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.551→47.177 Å
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Refine LS restraints |
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LS refinement shell |
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