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Yorodumi- PDB-6kae: Crosslinked alpha(Fe-CO)-beta(Ni) human hemoglobin A in the T qua... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kae | ||||||
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Title | Crosslinked alpha(Fe-CO)-beta(Ni) human hemoglobin A in the T quaternary structure at 95 K: Light | ||||||
Components | (Hemoglobin subunit ...) x 2 | ||||||
Keywords | OXYGEN TRANSPORT / Hemoglobin / Photolysis / Hybrid | ||||||
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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Shibayama, N. / Park, S.Y. / Ohki, M. / Sato-Tomita, A. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Direct observation of ligand migration within human hemoglobin at work. Authors: Shibayama, N. / Sato-Tomita, A. / Ohki, M. / Ichiyanagi, K. / Park, S.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kae.cif.gz | 270.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kae.ent.gz | 215.7 KB | Display | PDB format |
PDBx/mmJSON format | 6kae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kae_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 6kae_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 6kae_validation.xml.gz | 60.1 KB | Display | |
Data in CIF | 6kae_validation.cif.gz | 85.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/6kae ftp://data.pdbj.org/pub/pdb/validation_reports/ka/6kae | HTTPS FTP |
-Related structure data
Related structure data | 6ka9C 6kahC 6kaiC 6kaoC 6kapC 6kaqC 6karC 6kasC 6katC 6kauC 6kavC 6l5vC 6l5wC 6l5xC 6l5yC 6lcwC 6lcxC 1j3zS C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
-Hemoglobin subunit ... , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905 #2: Protein | Mass: 15890.198 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871 |
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-Non-polymers , 5 types, 1368 molecules
#3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-CMO / #5: Chemical | ChemComp-HNI / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.44 Å3/Da / Density % sol: 49.5 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 6.6 Details: 18%w/v PEG3350, 50 mM citrate-ammonium buffer, 150 mM dipotassium sulfate |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 15, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→19.9 Å / Num. obs: 207349 / % possible obs: 98.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 11.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.04 / Rrim(I) all: 0.088 / Net I/σ(I): 10.2 / Num. measured all: 877794 / Scaling rejects: 20 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J3Z Resolution: 1.45→19.899 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 19.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.09 Å2 / Biso mean: 18.1499 Å2 / Biso min: 4.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→19.899 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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