+Open data
-Basic information
Entry | Database: PDB / ID: 4x0j | ||||||
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Title | Trypanosoma brucei haptoglobin-haemoglobin receptor | ||||||
Components | Haptoglobin-hemoglobin receptor | ||||||
Keywords | PROTEIN TRANSPORT / Trypanosoma brucei / Haptoglobin-haemoglobin receptor | ||||||
Function / homology | Ferritin - #80 / Ferritin / Up-down Bundle / Mainly Alpha / Haptoglobin-hemoglobin receptor Function and homology information | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Lane-Serff, H. / MacGregor, P. / Lowe, E.D. / Carrington, M. / Higgins, M.K. | ||||||
Citation | Journal: Elife / Year: 2014 Title: Structural basis for ligand and innate immunity factor uptake by the trypanosome haptoglobin-haemoglobin receptor. Authors: Lane-Serff, H. / MacGregor, P. / Lowe, E.D. / Carrington, M. / Higgins, M.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x0j.cif.gz | 114.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x0j.ent.gz | 88.3 KB | Display | PDB format |
PDBx/mmJSON format | 4x0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4x0j_validation.pdf.gz | 436.4 KB | Display | wwPDB validaton report |
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Full document | 4x0j_full_validation.pdf.gz | 440.9 KB | Display | |
Data in XML | 4x0j_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 4x0j_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/4x0j ftp://data.pdbj.org/pub/pdb/validation_reports/x0/4x0j | HTTPS FTP |
-Related structure data
Related structure data | 4x0lC 5hu6C 4x0i 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 37 - 296 / Label seq-ID: 3 - 262
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-Components
#1: Protein | Mass: 28502.127 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: HpHbR / Production host: Escherichia coli (E. coli) / References: UniProt: I7BA99 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.23 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.15 M KBr, 30 % w/v PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→203.14 Å / Num. obs: 44672 / % possible obs: 97.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.64 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4X0I 4x0i Resolution: 1.85→203.14 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.942 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.144 / 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: 30.564 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→203.14 Å
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Refine LS restraints |
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