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- PDB-3ciu: Site-Selective Glycosylation of Cysteine-93 beta on the Surface o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ciu | ||||||
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Title | Site-Selective Glycosylation of Cysteine-93 beta on the Surface of Bovine Hemoglobin and its Application as a Novel Oxygen Therapeutic | ||||||
![]() | (Hemoglobin subunit ...) x 2 | ||||||
![]() | OXYGEN BINDING / Hemoglobin / glycosylation / site-selective / oxygen carrier / blood substitute / Heme / Iron / Oxygen transport / Polymorphism / Transport | ||||||
Function / homology | ![]() Scavenging of heme from plasma / Heme signaling / Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Cytoprotection by HMOX1 / Neutrophil degranulation / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding ...Scavenging of heme from plasma / Heme signaling / Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Cytoprotection by HMOX1 / Neutrophil degranulation / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bhatt, V.S. / Zhang, Y. / Sun, G. / Wang, P.G. / Palmer, A.F. | ||||||
![]() | ![]() Title: Site-Selective Glycosylation of Cysteine-93 beta on the Surface of Bovine Hemoglobin and its Application as a Novel Oxygen Therapeutic Authors: Bhatt, V.S. / Zhang, Y. / Sun, G. / Wang, P.G. / Palmer, A.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.2 KB | Display | ![]() |
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PDB format | ![]() | 96.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 30.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1g0aS 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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Unit cell |
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Components
-Hemoglobin subunit ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 15077.171 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 15977.382 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 4 types, 17 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/O.gif)
![](data/chem/img/5DP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/O.gif)
![](data/chem/img/5DP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-O / #5: Chemical | ChemComp-5DP / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.17 % |
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Crystal grow | Temperature: 293 K / Method: microbatch under oil / pH: 8.25 Details: 25 % Polyethylene glycol, monomethyl ether 2000, 0.2 M Trimethylamine N-oxide dehydrate and 0.1 M Tris, pH 8.25, Microbatch under oil, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jan 10, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→24.5 Å / Num. all: 7999 / Num. obs: 7354 / Redundancy: 3 % / Biso Wilson estimate: 91.2 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 3.5→3.6 Å / Redundancy: 2.85 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.4 / Num. unique all: 7710 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1G0A Resolution: 3.5→24.5 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.879 / SU B: 50.865 / SU ML: 0.767 / Cross valid method: THROUGHOUT / ESU R Free: 0.945 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 91.201 Å2
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Refinement step | Cycle: LAST / Resolution: 3.5→24.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.591 Å / Total num. of bins used: 20
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