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Yorodumi- PDB-1fcs: CRYSTAL STRUCTURE OF A DISTAL SITE DOUBLE MUTANT OF SPERM WHALE M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fcs | ||||||
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Title | CRYSTAL STRUCTURE OF A DISTAL SITE DOUBLE MUTANT OF SPERM WHALE MYOGLOBIN AT 1.6 ANGSTROMS RESOLUTION | ||||||
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: 1.6 Å | ||||||
Authors | Rizzi, M. / Bolognesi, M. / Coda, A. / Cutruzzola, F. / Travaglini Allocatelli, C. / Brancaccio, A. / Brunori, M. | ||||||
Citation | Journal: FEBS Lett. / Year: 1993 Title: Crystal structure of a distal site double mutant of sperm whale myoglobin at 1.6 A resolution. Authors: Rizzi, M. / Bolognesi, M. / Coda, A. / Cutruzzola, F. / Allocatelli, C.T. / Brancaccio, A. / Brunori, M. #1: Journal: FEBS Lett. / Year: 1991 Title: Control and Recognition of Anionic Ligands in Myoglobin Authors: Cutruzzola, F. / Allocatelli, C.T. / Ascenzi, P. / Bolognesi, M. / Sligar, S.G. / Brunori, M. #2: Journal: J.Mol.Recog. / Year: 1991 Title: Binding Mode of Azide to Ferric Aplysia Limacina Myoglobin. Crystallographic Analysis at 1.9 Angstroms Resolution Authors: Mattevi, A. / Gatti, G. / Coda, A. / Rizzi, M. / Ascenzi, P. / Brunori, M. / Bolognesi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fcs.cif.gz | 47.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fcs.ent.gz | 33.3 KB | Display | PDB format |
PDBx/mmJSON format | 1fcs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fcs_validation.pdf.gz | 837.1 KB | Display | wwPDB validaton report |
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Full document | 1fcs_full_validation.pdf.gz | 841 KB | Display | |
Data in XML | 1fcs_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 1fcs_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/1fcs ftp://data.pdbj.org/pub/pdb/validation_reports/fc/1fcs | 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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Atom site foot note | 1: ARG 45 AND ARG 67 POINT OUT THE DISTAL SITE AND ARE KEPT IN THIS POSITION BY INTERACTIONS WITH A SULFATE ION LOCATED AMONGST THE TWO ON THE PROTEIN SURFACE. |
-Components
#1: Protein | Mass: 17382.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: SYNTHETIC GENE / References: UniProt: P02185 | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Water | ChemComp-HOH / | Compound details | ARG 45 AND ARG 67 POINT OUT THE DISTAL SITE AND ARE KEPT IN THIS POSITION BY INTERACTIONS WITH A ...ARG 45 AND ARG 67 POINT OUT THE DISTAL SITE AND ARE KEPT IN THIS POSITION BY INTERACTIO | Sequence details | SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.24 % |
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Crystal grow | *PLUS Method: other / Details: NMR |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 15 Å / Num. obs: 15938 / % possible obs: 53 % / Num. measured all: 62341 / Rmerge(I) obs: 0.052 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.6→15 Å /
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Refinement step | Cycle: LAST / Resolution: 1.6→15 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 15 Å / Num. reflection obs: 15938 / Rfactor obs: 0.197 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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