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Yorodumi- PDB-3s48: Human Alpha-Haemoglobin Complexed with the First NEAT Domain of I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s48 | ||||||
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Title | Human Alpha-Haemoglobin Complexed with the First NEAT Domain of IsdH from Staphylococcus aureus | ||||||
Components |
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Keywords | OXYGEN TRANSPORT/PROTEIN BINDING / haemoglobin / NEAT domain / IsdH / protein-protein complex / host-pathogen interaction / OXYGEN TRANSPORT-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information nitric oxide transport / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / hydrogen peroxide catabolic process / oxygen carrier activity ...nitric oxide transport / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / hydrogen peroxide catabolic process / oxygen carrier activity / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / peroxidase activity / blood microparticle / iron ion binding / heme binding / extracellular space / extracellular exosome / extracellular region / membrane / cytosol Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å | ||||||
Authors | Kumar, K.K. / Jacques, D.A. / Caradoc-Davies, T.T. / Guss, J.M. / Gell, D.A. | ||||||
Citation | Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2014 Title: The structure of alpha-haemoglobin in complex with a haemoglobin-binding domain from Staphylococcus aureus reveals the elusive alpha-haemoglobin dimerization interface Authors: Krishna Kumar, K. / Jacques, D.A. / Guss, J.M. / Gell, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s48.cif.gz | 243.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s48.ent.gz | 198.8 KB | Display | PDB format |
PDBx/mmJSON format | 3s48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3s48_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3s48_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3s48_validation.xml.gz | 22 KB | Display | |
Data in CIF | 3s48_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s4/3s48 ftp://data.pdbj.org/pub/pdb/validation_reports/s4/3s48 | HTTPS FTP |
-Related structure data
Related structure data | 3ovuS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18904.824 Da / Num. of mol.: 2 / Fragment: first NEAT domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MSSA476 / Gene: isdH / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6G8J7 #2: Protein | Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: Blood / References: UniProt: P69905 #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 64.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M sodium sulphate, 0.1M Bis Tris propane, 16%(w/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2011 |
Radiation | Monochromator: Double crystal (Si111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→89.74 Å / Num. all: 16833 / Num. obs: 16833 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3.05→3.1 Å / % possible all: 99.46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OVU Resolution: 3.05→89.74 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.903 / SU B: 46.168 / SU ML: 0.373 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.43 / 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: 134.995 Å2
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Refinement step | Cycle: LAST / Resolution: 3.05→89.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.051→3.13 Å / Total num. of bins used: 20
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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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