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Yorodumi- PDB-5l4v: Crystal structure of FimH lectin domain in complex with 3-Deoxy-H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l4v | ||||||
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Title | Crystal structure of FimH lectin domain in complex with 3-Deoxy-Heptylmannoside | ||||||
Components | Protein FimH | ||||||
Keywords | SUGAR BINDING PROTEIN / FimH / Type 1 pilus / urinary tract infection / UTI / carbohydrate / lectin / mannose / cell adhesion | ||||||
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: 2.99 Å | ||||||
Authors | Jakob, R.P. / Zihlmann, P. / Rabbani, S. / Maier, T. / Ernst, T. | ||||||
Citation | Journal: To Be Published Title: High-Affinity Carbohydrate-Lectin Interactions: How Nature Makes it Possible Authors: Zihlmann, P. / Jiang, X. / Sager, C.P. / Fiege, B. / Jakob, R.P. / Siegrist, S. / Zalewski, A. / Rabbani, S. / Eris, D. / Silbermann, M. / Pang, L. / Muhlethaler, T. / Sharpe, T. / 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 | 5l4v.cif.gz | 189.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l4v.ent.gz | 153.5 KB | Display | PDB format |
PDBx/mmJSON format | 5l4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l4v_validation.pdf.gz | 937.8 KB | Display | wwPDB validaton report |
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Full document | 5l4v_full_validation.pdf.gz | 943.3 KB | Display | |
Data in XML | 5l4v_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 5l4v_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/5l4v ftp://data.pdbj.org/pub/pdb/validation_reports/l4/5l4v | HTTPS FTP |
-Related structure data
Related structure data | 5l4tC 5l4uC 5l4wC 5l4xC 5l4yC 4xo8S 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 16916.828 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: fimH, b4320, JW4283 / Plasmid: pTRC99a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08191 #2: Sugar | #3: 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: 2.88 Å3/Da / Density % sol: 57.35 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop Details: 0.2 M (NH4)2SO4, 0.1 M Hepes pH 7 and 25-30% PEG3350 |
-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: Jun 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→47.67 Å / Num. obs: 11564 / % possible obs: 98.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 28.27 Å2 / CC1/2: 0.86 / Rmerge(I) obs: 0.301 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 2.99→3.17 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 1.3 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XO8 Resolution: 2.99→47.67 Å / Cor.coef. Fo:Fc: 0.7409 / Cor.coef. Fo:Fc free: 0.7257 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.414
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Displacement parameters | Biso mean: 25.81 Å2
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Refine analyze | Luzzati coordinate error obs: 0.535 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.99→47.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.99→3.27 Å / Total num. of bins used: 6
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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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