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Yorodumi- PDB-5jdo: T. congolense haptoglobin-haemoglobin receptor in complex with ha... -
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-Basic information
Entry | Database: PDB / ID: 5jdo | ||||||
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Title | T. congolense haptoglobin-haemoglobin receptor in complex with haemoglobin | ||||||
Components |
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Keywords | OXYGEN TRANSPORT / Trypanosome / haptoglobin-haemoglobin receptor / haemoglobin / epimastigote | ||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / platelet aggregation / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / carbon dioxide transport / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / response to hydrogen peroxide / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / ficolin-1-rich granule lumen / blood microparticle / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Trypanosoma congolense (eukaryote) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Lane-Serff, H. / Higgins, M.K. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Elife / Year: 2016 Title: Evolutionary diversification of the trypanosome haptoglobin-haemoglobin receptor from an ancestral haemoglobin receptor. Authors: Lane-Serff, H. / MacGregor, P. / Peacock, L. / Macleod, O.J. / Kay, C. / Gibson, W. / Higgins, M.K. / Carrington, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jdo.cif.gz | 418.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jdo.ent.gz | 346.1 KB | Display | PDB format |
PDBx/mmJSON format | 5jdo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jdo_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5jdo_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5jdo_validation.xml.gz | 37.7 KB | Display | |
Data in CIF | 5jdo_validation.cif.gz | 50.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/5jdo ftp://data.pdbj.org/pub/pdb/validation_reports/jd/5jdo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Haptoglobin-haemoglobin ... , 2 types, 2 molecules AB
#1: Protein | Mass: 26563.549 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma congolense (eukaryote) / Gene: TCIL3000_10_2930 / Production host: Escherichia coli (E. coli) / References: UniProt: G0UVW6 |
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#2: Protein | Mass: 26117.139 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma congolense (eukaryote) / Gene: TCIL3000_10_2930 / Production host: Escherichia coli (E. coli) / References: UniProt: G0UVW6 |
-Hemoglobin subunit ... , 4 types, 4 molecules CDEF
#3: Protein | Mass: 15150.353 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / Production host: Homo sapiens (human) / References: UniProt: P69905 |
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#4: Protein | Mass: 15791.067 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Production host: Homo sapiens (human) / References: UniProt: P68871 |
#5: Protein | Mass: 14993.159 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / Production host: Homo sapiens (human) / References: UniProt: P69905 |
#6: Protein | Mass: 15652.920 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Production host: Homo sapiens (human) / References: UniProt: P68871 |
-Non-polymers , 2 types, 8 molecules
#7: Chemical | ChemComp-HEM / #8: Chemical | ChemComp-OXY / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.79 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium citrate pH 5, 8% w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→102.41 Å / Num. obs: 26536 / % possible obs: 99 % / Redundancy: 2.7 % / Biso Wilson estimate: 93.75 Å2 / Rpim(I) all: 0.073 / Net I/σ(I): 7.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4E40 and 1HH0 Resolution: 3.2→102.41 Å / Cor.coef. Fo:Fc: 0.9152 / Cor.coef. Fo:Fc free: 0.9127 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.412
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Displacement parameters | Biso mean: 87.29 Å2
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Refine analyze | Luzzati coordinate error obs: 0.706 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.2→102.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.33 Å / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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