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Yorodumi- PDB-1ycb: DISTAL POCKET POLARITY IN LIGAND BINDING TO MYOGLOBIN: DEOXY AND ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ycb | ||||||
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Title | DISTAL POCKET POLARITY IN LIGAND BINDING TO MYOGLOBIN: DEOXY AND CARBONMONOXY FORMS OF A THREONINE68 (E11) MUTANT INVESTIGATED BY X-RAY CRYSTALLOGRAPHY AND INFRARED SPECTROSCOPY | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN STORAGE | ||||||
Function / homology | Function and homology information Intracellular oxygen transport / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / oxygen transport / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding ...Intracellular oxygen transport / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / oxygen transport / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Cameron, A.D. / Smerdon, S.J. / Wilkinson, A.J. / Habash, J. / Helliwell, J.R. | ||||||
Citation | Journal: Biochemistry / Year: 1993 Title: Distal pocket polarity in ligand binding to myoglobin: deoxy and carbonmonoxy forms of a threonine68(E11) mutant investigated by X-ray crystallography and infrared spectroscopy. Authors: Cameron, A.D. / Smerdon, S.J. / Wilkinson, A.J. / Habash, J. / Helliwell, J.R. / Li, T. / Olson, J.S. #1: Journal: Biochemistry / Year: 1992 Title: High Resolution X-Ray Structures of Pig Metmyoglobin and Two Cd3 Mutants Mb(Lys45-> Arg) and Mb(Lys45-> Ser) Authors: Oldfield, T.J. / Smerdon, S.J. / Dauter, Z. / Petratos, K. / Wilson, K.S. / Wilkinson, A.J. #2: Journal: Biochemistry / Year: 1991 Title: Distal Polarity in Ligand Binding to Myoglobin: Structural and Functional Characterization of a Threonine68(E11) Mutant Authors: Smerdon, S.J. / Dodson, G.G. / Wilkinson, A.J. / Gibson, Q.H. / Blackmore, R.S. / Carver, T.E. / Olson, J.S. #3: Journal: Acta Crystallogr.,Sect.B / Year: 1990 Title: Determination of the Crystal Structure of Recombinant Pig Myoglobin by Molecular Replacement and its Refinement Authors: Smerdon, S.J. / Oldfield, T.J. / Dodson, E.J. / Dodson, G.G. / Hubbard, R.E. / Wilkinson, A.J. #4: Journal: Protein Eng. / Year: 1988 Title: Apomyoglobin as a Molecular Recognition Surface: Expression, Reconstitution and Crystallisation of Recombinant Porcine Myoglobin in Escherichia Coli Authors: Dodson, G.G. / Hubbard, R.E. / Oldfield, T.J. / Smerdon, S.J. / Wilkinson, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ycb.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ycb.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ycb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/1ycb ftp://data.pdbj.org/pub/pdb/validation_reports/yc/1ycb | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Atom site foot note | 1: PHE A 151 - GLN A 152 OMEGA ANGLE = 146.397 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
-Components
#1: Protein | Mass: 16985.418 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P02189 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal grow | *PLUS pH: 7.1 / Method: vapor diffusion, hanging drop / Details: under 1 atm of argon | ||||||||||||||||||||||||||||||
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Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.1 Å / Num. obs: 18251 / Rmerge(I) obs: 0.111 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.1→8 Å / σ(F): 0 Details: THIS STRUCTURE WAS REFINED AGAINST LAUE DATA TO 2.1 ANGSTROMS RESOLUTION. THE DATA SET IS 63% COMPLETE OVERALL BUT ONLY 38% OF REFLECTIONS ARE PRESENT BELOW 2DMIN. AS A RESULT THE ELECTRON ...Details: THIS STRUCTURE WAS REFINED AGAINST LAUE DATA TO 2.1 ANGSTROMS RESOLUTION. THE DATA SET IS 63% COMPLETE OVERALL BUT ONLY 38% OF REFLECTIONS ARE PRESENT BELOW 2DMIN. AS A RESULT THE ELECTRON DENSITY MAPS HAVE BREAKS PERIODICALLY ALONG THE MAIN CHAIN. THOSE ATOMS WHICH COULD NOT BE OBSERVED IN ANY MAP HAVE BEEN ASSIGNED AN OCCUPANCY OF 0.0. DURING THE COURSE OF REFINEMENT REASONABLY TIGHT RESTRAINTS WERE APPLIED TO THE GEOMETRY WHILE MOST ATTENTION WAS PAID TO THE HAEM GROUP AND ITS ENVIRONMENT. THIS STRATEGY WAS ADOPTED AS THE PURPOSE OF THE STUDY WAS TO DEFINE THE LOCATION OF WATER MOLECULES IN THE DISTAL POCKET.
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Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 8 Å / Num. reflection all: 18200 / σ(F): 0 / Rfactor all: 0.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |