+Open data
-Basic information
Entry | Database: PDB / ID: 2jh1 | ||||||
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Title | Crystal structure of Toxoplasma gondii micronemal protein 1 | ||||||
Components | MICRONEMAL PROTEIN 1 | ||||||
Keywords | CELL ADHESION / MIC1 / MICRONEME / MAR DOMAIN / CELL INVASION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | TOXOPLASMA GONDII (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Blumenschein, T.M.A. / Friedrich, N. / Childs, R.A. / Saouros, S. / Carpenter, E.P. / Campanero-Rhodes, M.A. / Simpson, P. / Koutroukides, T. / Blackman, M.J. / Feizi, T. ...Blumenschein, T.M.A. / Friedrich, N. / Childs, R.A. / Saouros, S. / Carpenter, E.P. / Campanero-Rhodes, M.A. / Simpson, P. / Koutroukides, T. / Blackman, M.J. / Feizi, T. / Soldati-Favre, D. / Matthews, S. | ||||||
Citation | Journal: Embo J. / Year: 2007 Title: Atomic Resolution Insight Into Host Cell Recognition by Toxoplasma Gondii. Authors: Blumenschein, T.M.A. / 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. / ...Authors: Blumenschein, T.M.A. / 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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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jh1.cif.gz | 62.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jh1.ent.gz | 49.9 KB | Display | PDB format |
PDBx/mmJSON format | 2jh1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/2jh1 ftp://data.pdbj.org/pub/pdb/validation_reports/jh/2jh1 | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 27172.219 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) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI DE3 / References: UniProt: O00834 | ||||||
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#2: Chemical | ChemComp-ACT / #3: Chemical | #4: Chemical | #5: 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: 3.48 Å3/Da / Density % sol: 64.6 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.6 Details: VAPOUR DIFFUSION, HANGING DROP 3.6 M AMMONIUM ACETATE, 100 MM BIS-TRIS-PROPANE PH 7.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 26, 2006 / Details: COLLIMATOR, MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→18 Å / Num. obs: 30153 / % possible obs: 96.6 % / Observed criterion σ(I): -3.7 / Redundancy: 5.1 % / Rsym value: 0.08 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.31 / % possible all: 76.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→17.49 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.63 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS DENSITY ON A TWO FOLD AXIS ADJACENT TO RESIDUE 111 WHICH COULD BE DUE TO A PARTIALLY DISORDERED GLYCEROL MOLECULE.
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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: 27.77 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→17.49 Å
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Refine LS restraints |
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