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Yorodumi- PDB-7mzs: Crystal structure of the UcaD lectin-binding domain in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mzs | ||||||
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Title | Crystal structure of the UcaD lectin-binding domain in complex with galactose | ||||||
Components | Fimbrial adhesin UcaD | ||||||
Keywords | SUGAR BINDING PROTEIN / lectin / cell adhesion | ||||||
Function / homology | Fimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / pilus / cell adhesion / alpha-D-galactopyranose / Fimbrial adhesin Function and homology information | ||||||
Biological species | Proteus mirabilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Ve, T. / Lo, A.W. / Schembri, M.A. / Kobe, B. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Plos Pathog. / Year: 2022 Title: Ucl fimbriae regulation and glycan receptor specificity contribute to gut colonisation by extra-intestinal pathogenic Escherichia coli. Authors: Hancock, S.J. / Lo, A.W. / Ve, T. / Day, C.J. / Tan, L. / Mendez, A.A. / Phan, M.D. / Nhu, N.T.K. / Peters, K.M. / Richards, A.C. / Fleming, B.A. / Chang, C. / Ngu, D.H.Y. / Forde, B.M. / ...Authors: Hancock, S.J. / Lo, A.W. / Ve, T. / Day, C.J. / Tan, L. / Mendez, A.A. / Phan, M.D. / Nhu, N.T.K. / Peters, K.M. / Richards, A.C. / Fleming, B.A. / Chang, C. / Ngu, D.H.Y. / Forde, B.M. / Haselhorst, T. / Goh, K.G.K. / Beatson, S.A. / Jennings, M.P. / Mulvey, M.A. / Kobe, B. / Schembri, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mzs.cif.gz | 106.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mzs.ent.gz | 66 KB | Display | PDB format |
PDBx/mmJSON format | 7mzs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/7mzs ftp://data.pdbj.org/pub/pdb/validation_reports/mz/7mzs | HTTPS FTP |
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-Related structure data
Related structure data | 7mzoC 7mzpC 7mzqC 7mzrC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21985.908 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus mirabilis (bacteria) / Gene: NCTC10975_02625 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A2X2BLR9 | ||||
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#2: Sugar | ChemComp-GLA / | ||||
#3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium citrate buffer pH 4.5-5.5, 2-3 M NaCl / PH range: 4.5-5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→56.12 Å / Num. obs: 23071 / % possible obs: 99.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 13.04 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.077 / Rrim(I) all: 0.151 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.72→1.75 Å / Rmerge(I) obs: 1.114 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1237 / CC1/2: 0.291 / Rpim(I) all: 0.687 / Rrim(I) all: 1.319 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: UcaD Resolution: 1.72→39.68 Å / SU ML: 0.191 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.1686 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 16.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→39.68 Å
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Refine LS restraints |
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LS refinement shell |
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