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- PDB-6kah: Crosslinked alpha(Ni)-beta(Fe-CO) human hemoglobin A in the T qua... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6kah | ||||||
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Title | Crosslinked alpha(Ni)-beta(Fe-CO) human hemoglobin A in the T quaternary structure at 95 K: Dark | ||||||
![]() | (Hemoglobin subunit ...) x 2 | ||||||
![]() | OXYGEN TRANSPORT / Hemoglobin / Photolysis / Hybrid | ||||||
Function / homology | ![]() nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shibayama, N. / Park, S.Y. / Ohki, M. / Sato-Tomita, A. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 272.6 KB | Display | ![]() |
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PDB format | ![]() | 217.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.1 MB | Display | ![]() |
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Full document | ![]() | 3.1 MB | Display | |
Data in XML | ![]() | 62.1 KB | Display | |
Data in CIF | ![]() | 89 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ka9C ![]() 6kaeC ![]() 6kaiC ![]() 6kaoC ![]() 6kapC ![]() 6kaqC ![]() 6karC ![]() 6kasC ![]() 6katC ![]() 6kauC ![]() 6kavC ![]() 6l5vC ![]() 6l5wC ![]() 6l5xC ![]() 6l5yC ![]() 6lcwC ![]() 6lcxC ![]() 1j40S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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) ![]() #2: Protein | Mass: 15890.198 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 5 types, 1526 molecules ![](data/chem/img/HNI.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/CMO.gif)
![](data/chem/img/2FU.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/CMO.gif)
![](data/chem/img/2FU.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-HNI / #4: Chemical | ChemComp-HEM / #5: Chemical | ChemComp-CMO / #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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.42 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 6.6 Details: 20%w/v PEG 3350, 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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
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→19.85 Å / Num. obs: 201015 / % possible obs: 97.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 11.64 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.032 / Rrim(I) all: 0.071 / Net I/σ(I): 14.5 / Num. measured all: 909011 / Scaling rejects: 104 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1J40 Resolution: 1.45→19.85 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 19.05
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.65 Å2 / Biso mean: 17.2216 Å2 / Biso min: 4.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→19.85 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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