- PDB-1ut0: CRYSTAL STRUCTURE OF CYTOGLOBIN: THE FOURTH GLOBIN TYPE DISCOVERE... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1ut0
Title
CRYSTAL STRUCTURE OF CYTOGLOBIN: THE FOURTH GLOBIN TYPE DISCOVERED IN MAN DISPLAYS HEME HEXA-COORDINATION
Components
CYTOGLOBIN
Keywords
OXYGEN TRANSPORT / HEMOGLOBIN
Function / homology
Function and homology information
Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donor / fatty acid peroxidase activity / nitric oxide dioxygenase activity, heme protein as donor / negative regulation of hepatic stellate cell activation / Intracellular oxygen transport / nitric oxide catabolic process / negative regulation of collagen biosynthetic process / carbon monoxide binding / negative regulation of fibroblast migration / catalase activity ...Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donor / fatty acid peroxidase activity / nitric oxide dioxygenase activity, heme protein as donor / negative regulation of hepatic stellate cell activation / Intracellular oxygen transport / nitric oxide catabolic process / negative regulation of collagen biosynthetic process / carbon monoxide binding / negative regulation of fibroblast migration / catalase activity / superoxide dismutase / superoxide dismutase activity / fatty acid oxidation / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / eNOS activation / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / response to oxidative stress / oxidoreductase activity / response to hypoxia / neuron projection / iron ion binding / neuronal cell body / heme binding / nucleus / cytosol / cytoplasm Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Compound details
ENGINEERED MUTATION IN CHAIN A, CYS 38 TO SER 38 ENGINEERED MUTATION IN CHAIN A, CYS 83 TO SER 83 ...ENGINEERED MUTATION IN CHAIN A, CYS 38 TO SER 38 ENGINEERED MUTATION IN CHAIN A, CYS 83 TO SER 83 ENGINEERED MUTATION IN CHAIN B, CYS 38 TO SER 38 ENGINEERED MUTATION IN CHAIN B, CYS 83 TO SER 83
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.03 Å3/Da / Density % sol: 37 %
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.934 Å / Relative weight: 1
Reflection
Resolution: 2.1→50 Å / Num. obs: 341899 / % possible obs: 99.5 % / Redundancy: 2 %
Reflection shell
Resolution: 2.1→2.24 Å
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Processing
Software
Name
Classification
REFMAC
refinement
MOSFLM
datareduction
SCALA
datascaling
Refinement
Method to determine structure: OTHER / Resolution: 2.1→50 Å / SU B: 6.194 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.215 / Details: NONE
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26166
1034
5.1 %
RANDOM
Rwork
0.21345
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obs
0.21591
19111
95.87 %
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Displacement parameters
Biso mean: 22.233 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.01 Å2
0 Å2
0 Å2
2-
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0 Å2
0 Å2
3-
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0 Å2
Refinement step
Cycle: LAST / Resolution: 2.1→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2464
0
112
98
2674
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