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Yorodumi- PDB-3f5e: Crystal structure of Toxoplasma gondii micronemal protein 1 bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f5e | |||||||||
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Title | Crystal structure of Toxoplasma gondii micronemal protein 1 bound to 2'F-3'SiaLacNAc1-3 | |||||||||
Components | Micronemal protein 1 | |||||||||
Keywords | CELL ADHESION / cellular adhesion / micronemal protein 1 / toxoplasma gondii / carbohydrate / fluorine / Cytoplasmic vesicle / Lectin / Virulence | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Toxoplasma gondii (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Garnett, J.A. / Liu, Y. / Feizi, T. / Matthews, S.J. | |||||||||
Citation | Journal: Protein Sci. / Year: 2009 Title: Detailed insights from microarray and crystallographic studies into carbohydrate recognition by microneme protein 1 (MIC1) of Toxoplasma gondii. Authors: Garnett, J.A. / Liu, Y. / Leon, E. / Allman, S.A. / Friedrich, N. / Saouros, S. / Curry, S. / Soldati-Favre, D. / Davis, B.G. / Feizi, T. / Matthews, S. #1: Journal: Embo J. / Year: 2007 Title: Atomic resolution insight into host cell recognition by Toxoplasma gondii. Authors: Blumenschein, T.M. / Friedrich, N. / Childs, R.A. / Saouros, S. / Carpenter, E.P. / Campanero-Rhodes, M.A. / Simpson, P. / Chai, W. / Koutroukides, T. / Blackman, M.J. / Feizi, T. / Soldati- ...Authors: Blumenschein, T.M. / Friedrich, N. / Childs, R.A. / Saouros, S. / Carpenter, E.P. / Campanero-Rhodes, M.A. / Simpson, P. / Chai, W. / Koutroukides, T. / Blackman, M.J. / Feizi, T. / Soldati-Favre, D. / Matthews, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f5e.cif.gz | 68.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f5e.ent.gz | 48 KB | Display | PDB format |
PDBx/mmJSON format | 3f5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f5e_validation.pdf.gz | 812.9 KB | Display | wwPDB validaton report |
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Full document | 3f5e_full_validation.pdf.gz | 816.5 KB | Display | |
Data in XML | 3f5e_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 3f5e_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/3f5e ftp://data.pdbj.org/pub/pdb/validation_reports/f5/3f5e | HTTPS FTP |
-Related structure data
Related structure data | 3f53C 3f5aC 2jh1S 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 on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 27266.010 Da / Num. of mol.: 1 / Fragment: N-terminal domain: Residues 17-262 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: RH / Gene: MIC1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): origami / References: UniProt: O00834 |
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#2: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-2-deoxy-2-fluoro-beta-D-galactopyranose-(1-3)-2-acetamido-2- ...N-acetyl-alpha-neuraminic acid-(2-3)-2-deoxy-2-fluoro-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 205 molecules
#3: Chemical | ChemComp-CL / | ||||
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#4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.56 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 3.6M Ammonium acetate, 100mM Bis/tris-propane, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 19, 2007 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2→31.73 Å / Num. obs: 23986 / % possible obs: 99.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 22.268 Å2 / Rsym value: 0.076 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 5.6 / Num. unique all: 3769 / Rsym value: 0.222 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2JH1 Resolution: 2→29.66 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.628 / SU ML: 0.068 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.124 / 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: 22.106 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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