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Yorodumi- PDB-1mnk: INTERACTIONS AMONG RESIDUES CD3, E7, E10 AND E11 IN MYOGLOBINS: A... -
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-Basic information
Entry | Database: PDB / ID: 1mnk | ||||||
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Title | INTERACTIONS AMONG RESIDUES CD3, E7, E10 AND E11 IN MYOGLOBINS: ATTEMPTS TO SIMULATE THE O2 AND CO BINDING PROPERTIES OF APLYSIA MYOGLOBIN | ||||||
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 / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity ...Intracellular oxygen transport / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Krzywda, S. / Wilkinson, A.J. | ||||||
Citation | Journal: Biochemistry / Year: 1995 Title: Interactions among residues CD3, E7, E10, and E11 in myoglobins: attempts to simulate the ligand-binding properties of Aplysia myoglobin. Authors: Smerdon, S.J. / Krzywda, S. / Brzozowski, A.M. / Davies, G.J. / Wilkinson, A.J. / Brancaccio, A. / Cutruzzola, F. / Allocatelli, C.T. / Brunori, M. / Li, T. / Brantley Jr., R.E. / Carver, T. ...Authors: Smerdon, S.J. / Krzywda, S. / Brzozowski, A.M. / Davies, G.J. / Wilkinson, A.J. / Brancaccio, A. / Cutruzzola, F. / Allocatelli, C.T. / Brunori, M. / Li, T. / Brantley Jr., R.E. / Carver, T.E. / Eich, R.F. / Singleton, E. / Olson, J.S. #1: Journal: Biochemistry / Year: 1993 Title: Distal Pocket Polarity in Ligand Binding to Myoglobin: Deoxy and Carbonmonoxy Forms of 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. #2: 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. #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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mnk.cif.gz | 78.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mnk.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 1mnk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mnk_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1mnk_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1mnk_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 1mnk_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/1mnk ftp://data.pdbj.org/pub/pdb/validation_reports/mn/1mnk | HTTPS FTP |
-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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.995734, 0.046053, 0.079955), Vector: Details | MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX CHAIN RESIDUES CHAIN RESIDUES RMSD M1 A 1 - A 153 B 1 - B 153 0.719 | |
-Components
#1: Protein | Mass: 16946.402 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 / | Nonpolymer details | THE HEME IRON IN MOLECULE A IS COORDINATE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.62 Å3/Da / Density % sol: 66.05 % | |||||||||||||||
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Crystal grow | *PLUS pH: 7.1 / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. obs: 23497 / % possible obs: 94.5 % / Rmerge(I) obs: 0.088 |
-Processing
Software |
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Refinement | Resolution: 2.2→10 Å /
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rfree: 0.237 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |