+Open data
-Basic information
Entry | Database: PDB / ID: 2y44 | ||||||
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Title | Crystal structure of GARP from Trypanosoma congolense | ||||||
Components | GLUTAMIC ACID/ALANINE-RICH PROTEIN | ||||||
Keywords | MEMBRANE PROTEIN / SURFACE PROTEIN | ||||||
Function / homology | Trypanosoma glutamic acid/alanine-rich protein / Glutamic acid/alanine-rich protein of Trypanosoma / Ferritin - #80 / Ferritin / Up-down Bundle / Mainly Alpha / IODIDE ION / Alanine-rich surface protein / Glutamic acid/alanine-rich protein Function and homology information | ||||||
Biological species | TRYPANOSOMA CONGOLENSE (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.65 Å | ||||||
Authors | Loveless, B.C. / Mason, J.W. / Sakurai, T. / Inoue, N. / Razavi, M. / Pearson, T.W. / Boulanger, M.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structural Characterization and Epitope Mapping of the Glutamic Acid/Alanine-Rich Protein from Trypanosoma Congolense: Defining Assembly on the Parasite Cell Surface. Authors: Loveless, B.C. / Mason, J.W. / Sakurai, T. / Inoue, N. / Razavi, M. / Pearson, T.W. / Boulanger, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y44.cif.gz | 49.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y44.ent.gz | 37.4 KB | Display | PDB format |
PDBx/mmJSON format | 2y44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y44_validation.pdf.gz | 432 KB | Display | wwPDB validaton report |
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Full document | 2y44_full_validation.pdf.gz | 433.3 KB | Display | |
Data in XML | 2y44_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 2y44_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/2y44 ftp://data.pdbj.org/pub/pdb/validation_reports/y4/2y44 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19395.477 Da / Num. of mol.: 1 / Fragment: ECTODOMAIN, RESIDUES 40-224 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA CONGOLENSE (eukaryote) / Strain: IL3000 / Plasmid: PGEX-4T-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9U0E1, UniProt: Q07419*PLUS | ||||||
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#2: Chemical | ChemComp-IOD / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Sequence details | GENE CLONED FROM A SPECIFIC STRAIN AND WITH THE KNOWN LEVEL OF POLYMORPHISM IN THIS FAMILY OF ...GENE CLONED FROM A SPECIFIC STRAIN AND WITH THE KNOWN LEVEL OF POLYMORPHI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.6 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.54 |
Detector | Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→34.62 Å / Num. obs: 20523 / % possible obs: 93.1 % / Observed criterion σ(I): 2 / Redundancy: 7.86 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 6.85 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.5 / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.65→34.62 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.171 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.125 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.995 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→34.62 Å
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