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Yorodumi- PDB-6l5w: Carbonmonoxy human hemoglobin C in the R quaternary structure at ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l5w | ||||||
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Title | Carbonmonoxy human hemoglobin C in the R quaternary structure at 140 K: Light (2 min) | ||||||
Components |
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Keywords | OXYGEN TRANSPORT / Hemoglobin / Photolysis | ||||||
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: 1.5 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 | 6l5w.cif.gz | 134.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l5w.ent.gz | 102.6 KB | Display | PDB format |
PDBx/mmJSON format | 6l5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l5w_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6l5w_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6l5w_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 6l5w_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l5/6l5w ftp://data.pdbj.org/pub/pdb/validation_reports/l5/6l5w | HTTPS FTP |
-Related structure data
Related structure data | 6ka9C 6kaeC 6kahC 6kaiC 6kaoC 6kapC 6kaqC 6karC 6kasC 6katC 6kauC 6kavC 6l5vC 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: 2.23 Å3/Da / Density % sol: 44.93 % |
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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: 140 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 S 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: 1.5→19.29 Å / Num. obs: 46381 / % possible obs: 100 % / Redundancy: 10.9 % / Biso Wilson estimate: 19.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.018 / Rrim(I) all: 0.06 / Net I/σ(I): 20.6 / Num. measured all: 507356 / Scaling rejects: 83 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3S66 Resolution: 1.5→19.222 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.34 Å2 / Biso mean: 30.0751 Å2 / Biso min: 11.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→19.222 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 23.7429 Å / Origin y: -19.8437 Å / Origin z: 11.3211 Å
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Refinement TLS group | Selection details: all |