+Open data
-Basic information
Entry | Database: PDB / ID: 4.0E+40 | ||||||
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Title | The haptoglobin-hemoglobin receptor of Trypanosoma congolense | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | TRANSPORT PROTEIN / haptoglobin-hemoglobin receptor / helical bundle / receptor / cell surface | ||||||
Function / homology | Haptoglobin-hemoglobin receptor / Ferritin - #80 / Ferritin / Up-down Bundle / Mainly Alpha / membrane / Uncharacterized protein Function and homology information | ||||||
Biological species | Trypanosoma congolense (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å | ||||||
Authors | Higgins, M.K. / Tkachenko, O. / Brown, A. / Reed, J. / Carrington, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Structure of the trypanosome haptoglobin-hemoglobin receptor and implications for nutrient uptake and innate immunity. Authors: Higgins, M.K. / Tkachenko, O. / Brown, A. / Reed, J. / Raper, J. / Carrington, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e40.cif.gz | 105.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e40.ent.gz | 87 KB | Display | PDB format |
PDBx/mmJSON format | 4e40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e40_validation.pdf.gz | 417.4 KB | Display | wwPDB validaton report |
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Full document | 4e40_full_validation.pdf.gz | 418.4 KB | Display | |
Data in XML | 4e40_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 4e40_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/4e40 ftp://data.pdbj.org/pub/pdb/validation_reports/e4/4e40 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26850.822 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma congolense (eukaryote) / Strain: IL3000 / Gene: TCIL3000_10_2930 / Production host: Escherichia coli (E. coli) / References: UniProt: G0UVW6 |
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#2: Water | ChemComp-HOH / |
Sequence details | PLEASE SEE PRIMARY CITATION FOR THE DETAILED EXPLANATION OF THE DISCREPANCIES BETWEEN THE UNIPROT ...PLEASE SEE PRIMARY CITATION FOR THE DETAILED EXPLANATIO |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.92 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 5% PEG 12,000, 0.1M sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 21, 2010 |
Radiation | Monochromator: single bounce / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.916 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→90.53 Å / Num. all: 46112 / Num. obs: 46112 / % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.6→90.53 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.984 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 27.906 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→90.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.598→1.64 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 27.799 Å / Origin y: -17.1458 Å / Origin z: -2.7568 Å
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