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- PDB-1fn3: CRYSTAL STRUCTURE OF NICKEL RECONSTITUTED HEMOGLOBIN-A CASE FOR P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fn3 | ||||||
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Title | CRYSTAL STRUCTURE OF NICKEL RECONSTITUTED HEMOGLOBIN-A CASE FOR PERMANENT, T-STATE HEMOGLOBIN | ||||||
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![]() | OXYGEN STORAGE/TRANSPORT / PERMANENT T-STATE / METAL ION COORDINATION / SUBUNIT INEQUIVALENCE / SPECTROSCOPY / CRYSTALLOGRAPHY. / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Venkateshrao, S. / Deepthi, S. / Pattabhi, V. / Manoharan, P.T. | ||||||
![]() | Journal: CURR.SCI. / Year: 2003 Title: Crystal Structure of Nickel Reconstituted Hemoglobin - A Case for Permanent, T-State Hemoglobin Authors: Venkateshrao, S. / Deepthi, S. / Pattabhi, V. / Manoharan, P.T. #1: ![]() Title: Oxygen Binding by Alpha(Fe2+)2Beta(Ni2+)2 Hemoglobin Crystals Authors: Bruno, S. / Bettati, S. / Manfredini, M. / Mozzarelli, A. / Bolognesi, M. / Deriu, D. / Rosano, C. / Tsuneshige, A. / Yonetani, T. / Henry, E. #2: ![]() Title: High Resolution Crystal Structures and Comparisons of T-State Deoxyhaemoglobin and Two Liganded T-State Haemoglobins:T(Alpha-Oxy)Haemoglobin and T(met)Haemoglobin Authors: Liddington, R. / Derewenda, Z. / Dodson, E. / Hubbard, R. / Dodson, G. #3: ![]() Title: Structure of Deoxy Quaternary Hemoglobin with Liganded Beta Subunits Authors: Luisi, B. / Liddington, B. / Fermi, G. / Shibayama, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.9 KB | Display | ![]() |
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PDB format | ![]() | 97.3 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 | ![]() | 24.9 KB | Display | |
Data in CIF | ![]() | 33 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1thbS 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
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Chemical | ChemComp-HNI / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.95 % | |||||||||||||||
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Crystal grow | pH: 7.2 / Details: pH 7.20 | |||||||||||||||
Crystal grow | *PLUS Method: batch method | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 5, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→19.81 Å / Num. obs: 19946 / % possible obs: 91.37 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.1549 / Net I/σ(I): 3.04 |
Reflection shell | Resolution: 2.48→2.6 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.7552 / Mean I/σ(I) obs: 0.07 / % possible all: 71.5 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 19.8 Å / % possible obs: 91.4 % / Redundancy: 3.8 % / Num. measured all: 75819 / Rmerge(I) obs: 0.155 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1THB Resolution: 2.48→8 Å / Cross valid method: FREE R / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.48→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.5 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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