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Yorodumi- PDB-3szk: Crystal Structure of Human metHaemoglobin Complexed with the Firs... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3szk | ||||||
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Title | Crystal Structure of Human metHaemoglobin Complexed with the First NEAT Domain of IsdH from Staphylococcus aureus | ||||||
Components |
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Keywords | OXYGEN TRANSPORT/PROTEIN BINDING / methaemoglobin / NEAT domain / IsdH / host-pathogen interaction / OXYGEN TRANSPORT-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information nitric oxide transport / cellular oxidant detoxification / hemoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / cellular oxidant detoxification / hemoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / regulation of blood pressure / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / response to hydrogen peroxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / platelet aggregation / oxygen binding / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / Factors involved in megakaryocyte development and platelet production / tertiary granule lumen / 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 | Staphylococcus aureus (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | ||||||
Authors | Jacques, D.A. / Kumar, K.K. / Guss, J.M. / Gell, D.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structural basis for hemoglobin capture by Staphylococcus aureus cell-surface protein, IsdH Authors: Krishna Kumar, K. / Jacques, D.A. / Pishchany, G. / Caradoc-Davies, T. / Spirig, T. / Malmirchegini, G.R. / Langley, D.B. / Dickson, C.F. / Mackay, J.P. / Clubb, R.T. / Skaar, E.P. / 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 | 3szk.cif.gz | 341.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3szk.ent.gz | 280.5 KB | Display | PDB format |
PDBx/mmJSON format | 3szk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3szk_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 3szk_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3szk_validation.xml.gz | 31.2 KB | Display | |
Data in CIF | 3szk_validation.cif.gz | 40.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/3szk ftp://data.pdbj.org/pub/pdb/validation_reports/sz/3szk | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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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: 1
NCS ensembles :
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-Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905 #2: Protein | Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871 #3: 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: MW2 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NW39 #4: Chemical | ChemComp-HEM / |
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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: 2.92 Å3/Da / Density % sol: 57.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M potassium thiocyanate, 0.1M Tris-bis propane, 20% PEG 3350 , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 2, 2011 |
Radiation | Monochromator: OSMIC VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.007→48.59 Å / Num. obs: 22644 / % possible obs: 95.76 % |
Reflection shell | Resolution: 3.007→3.085 Å / % possible all: 99.58 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DN1, 3OVU Resolution: 3.01→48.59 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.845 / SU B: 49.675 / SU ML: 0.395 / Cross valid method: THROUGHOUT / ESU R Free: 0.456 / 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: 54.914 Å2
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Refinement step | Cycle: LAST / Resolution: 3.01→48.59 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.007→3.085 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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