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Yorodumi- PDB-6kap: Carbonmonoxy human hemoglobin C in the R quaternary structure at ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kap | ||||||
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Title | Carbonmonoxy human hemoglobin C in the R quaternary structure at 95 K: Light | ||||||
Components |
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Keywords | OXYGEN TRANSPORT / Hemoglobin / Photolysis | ||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin 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 / Late endosomal microautophagy / 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 / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / 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 | 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 | 6kap.cif.gz | 133.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kap.ent.gz | 102.4 KB | Display | PDB format |
PDBx/mmJSON format | 6kap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kap_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6kap_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6kap_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 6kap_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/6kap ftp://data.pdbj.org/pub/pdb/validation_reports/ka/6kap | HTTPS FTP |
-Related structure data
Related structure data | 6ka9C 6kaeC 6kahC 6kaiC 6kaoC 6kaqC 6karC 6kasC 6katC 6kauC 6kavC 6l5vC 6l5wC 6l5xC 6l5yC 6lcwC 6lcxC 3s66S 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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Unit cell |
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-Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905 | ||||||
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#2: Protein | Mass: 15890.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871 | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.7 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 7.2 Details: 0.528 M sodium dihydrogen phosphate, 1.122 M dipotassium hydrogen phosphate, 10%v/v glycerol |
-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: Nov 23, 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→18.92 Å / Num. obs: 50776 / % possible obs: 99.8 % / Redundancy: 11.1 % / Biso Wilson estimate: 19.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.021 / Rrim(I) all: 0.07 / Net I/σ(I): 18 / Num. measured all: 562321 / Scaling rejects: 32 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3S66 Resolution: 1.45→18.92 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.74
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.87 Å2 / Biso mean: 29.8494 Å2 / Biso min: 12.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→18.92 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: 18
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Refinement TLS params. | Method: refined / Origin x: 23.6815 Å / Origin y: -19.766 Å / Origin z: 11.3054 Å
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Refinement TLS group | Selection details: all |