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Yorodumi- PDB-4buq: Crystal structure of wild type FimH lectin domain in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4buq | ||||||
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Title | Crystal structure of wild type FimH lectin domain in complex with heptyl alpha-D-mannopyrannoside | ||||||
Components | FIMH | ||||||
Keywords | CELL ADHESION / TYPE 1 FIMBRIAE / URINARY TRACT INFECTION / VARIABLE IMMUNOGLOBULIN FOLD | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ESCHERICHIA COLI UTI89 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.199 Å | ||||||
Authors | Rabbani, S. / Bouckaert, J. / Zalewski, A. / Preston, R. / Eid, S. / Thompson, A. / Puorger, C. / Glockshuber, R. / Ernst, B. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2013 Title: Validation of Reactivity Descriptors to Assess the Aromatic Stacking within the Tyrosine Gate of Fimh Authors: Roos, G. / Wellens, A. / Touaibia, M. / Yamakawa, N. / Geerlings, P. / Roy, R. / Wyns, L. / Bouckaert, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4buq.cif.gz | 78.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4buq.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 4buq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4buq_validation.pdf.gz | 629.6 KB | Display | wwPDB validaton report |
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Full document | 4buq_full_validation.pdf.gz | 629.3 KB | Display | |
Data in XML | 4buq_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 4buq_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/4buq ftp://data.pdbj.org/pub/pdb/validation_reports/bu/4buq | HTTPS FTP |
-Related structure data
Related structure data | 4attC 4aujC 4auuS 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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Unit cell |
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-Components
#1: Protein | Mass: 16916.828 Da / Num. of mol.: 2 / Fragment: LECTIN DOMAIN, RESIDUES 10-167 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI UTI89 (bacteria) / Plasmid: PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: A2IC68 #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: 2.89 Å3/Da / Density % sol: 57.4 % / Description: NONE |
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Crystal grow | pH: 7.8 Details: 5% PGA-LM, 0.1M TRIS-HCL PH 7.8, 30% V/V PEG 550 MME, 10 MM HEPTYL ALPHA-D-MANNOSE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 19, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→45 Å / Num. obs: 20238 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 7.24 % / Biso Wilson estimate: 25.87 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.33 |
Reflection shell | Resolution: 2.2→2.33 Å / Redundancy: 6.55 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.77 / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AUU Resolution: 2.199→45.139 Å / SU ML: 0.19 / σ(F): 1.99 / Phase error: 31.96 / Stereochemistry target values: ML
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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: 49.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.199→45.139 Å
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Refine LS restraints |
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LS refinement shell |
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