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Yorodumi- PDB-2cmm: STRUCTURAL ANALYSIS OF THE MYOGLOBIN RECONSTITUTED WITH IRON PORPHINE -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cmm | ||||||
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Title | STRUCTURAL ANALYSIS OF THE MYOGLOBIN RECONSTITUTED WITH IRON PORPHINE | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN TRANSPORT | ||||||
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 | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Sato, T. / Tanaka, N. / Moriyama, H. / Igarashi, N. / Neya, S. / Funasaki, N. / Iizuka, T. / Shiro, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1993 Title: Structural analysis of the myoglobin reconstituted with iron porphine. Authors: Neya, S. / Funasaki, N. / Sato, T. / Igarashi, N. / Tanaka, N. #1: Journal: Bull.Chem.Soc.Jpn. / Year: 1992 Title: The Crystal Structures of Cyanide Metmyoglobins Reconstituted with Iron(III) Complexes of Porphyrin, 5,10,15,20-Tetramethylporphyrin, and 5, 10,15,20-Tetraetylporphyrin Authors: Sato, T. / Tanaka, N. / Moriyama, H. / Matsumoto, O. / Takenaka, A. / Neya, S. / Funasaki, N. #2: Journal: Biochim.Biophys.Acta / Year: 1992 Title: Kinetic Studies on Co Binding to Reconstituted Myoglobins with Four Synthetic Hemes; Structural Control in Ligand Binding to Myoglobin Authors: Sato, T. / Tanaka, N. / Neya, S. / Funasaki, N. / Iizuka, T. / Shiro, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cmm.cif.gz | 43.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cmm.ent.gz | 31 KB | Display | PDB format |
PDBx/mmJSON format | 2cmm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cmm_validation.pdf.gz | 456.8 KB | Display | wwPDB validaton report |
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Full document | 2cmm_full_validation.pdf.gz | 465.8 KB | Display | |
Data in XML | 2cmm_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 2cmm_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/2cmm ftp://data.pdbj.org/pub/pdb/validation_reports/cm/2cmm | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17234.951 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / References: UniProt: P02185 |
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#2: Chemical | ChemComp-CYN / |
#3: Chemical | ChemComp-POR / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.94 % |
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Crystal grow | *PLUS Method: other / Details: NMR |
-Data collection
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 12640 / % possible obs: 89.5 % / Num. measured all: 37599 / Rmerge(I) obs: 0.0726 |
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-Processing
Software |
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Refinement | Rfactor Rwork: 0.187 / Rfactor obs: 0.187 / Highest resolution: 1.8 Å Details: THE SIDE GROUPS OF THE HEME WERE REMOVED COMPLETELY. ARG 45 IS DISPLACED LARGELY FROM THAT IN THE NATIVE AND MAKES OPEN A CHANNEL FOR THE LIGAND PENETRATION FORMED BY HIS 64, THR 67, VAL 68 AND HEME. | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.8 Å
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 7 Å / Num. reflection obs: 11808 / σ(F): 3 / Rfactor all: 0.187 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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