- PDB-2w6x: Crystal structure of Sperm Whale Myoglobin mutant YQRF in complex... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2w6x
Title
Crystal structure of Sperm Whale Myoglobin mutant YQRF in complex with Xenon
Components
MYOGLOBIN
Keywords
OXYGEN STORAGE / HYDROPHOBIC CAVITIES / DISTAL SITE POINT MUTATION / OXYGEN TRANSPORT / XENON DOCKING SITE / IRON / HEME / TRANSPORT / METAL-BINDING / MUSCLE PROTEIN
Function / homology
Function and homology information
Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Compound details
ENGINEERED RESIDUE IN CHAIN A, LEU 30 TO TYR ENGINEERED RESIDUE IN CHAIN A, HIS 65 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, LEU 30 TO TYR ENGINEERED RESIDUE IN CHAIN A, HIS 65 TO GLN ENGINEERED RESIDUE IN CHAIN A, THR 68 TO ARG ENGINEERED RESIDUE IN CHAIN A, ILE 108 TO PHE
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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: 2.4 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal grow
Method: vapor diffusion, hanging drop / pH: 8.7 Details: 2.8M AMMONIUM SULFATE, 0.1M TRIS/HCL, PH8.7, HANGING DROP AT RT
Resolution: 1.73→29.75 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.97 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.195
1118
5.1 %
RANDOM
Rwork
0.159
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obs
0.161
20739
100 %
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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