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Yorodumi- PDB-1mbo: Structure and refinement of oxymyoglobin at 1.6 angstroms resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mbo | |||||||||
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Title | Structure and refinement of oxymyoglobin at 1.6 angstroms resolution | |||||||||
Components | MYOGLOBIN | |||||||||
Keywords | OXYGEN STORAGE | |||||||||
Function / homology | Function and homology information hydrogen peroxide mediated signaling pathway / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Physeter catodon (sperm whale) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.6 Å | |||||||||
Authors | Phillips, S.E.V. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1980 Title: Structure and refinement of oxymyoglobin at 1.6 A resolution. Authors: Phillips, S.E. #1: Journal: Nature / Year: 1981 Title: Neutron Diffraction Reveals Oxygen-Histidine Hydrogen Bond in Oxymyoglobin Authors: Phillips, S.E.V. / Schoenborn, B.P. #3: Journal: Acta Crystallogr.,Sect.A (Supplement) / Year: 1978 Title: The Structure of Oxy-Myoglobin Authors: Phillips, S.E.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mbo.cif.gz | 50.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mbo.ent.gz | 36.2 KB | Display | PDB format |
PDBx/mmJSON format | 1mbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/1mbo ftp://data.pdbj.org/pub/pdb/validation_reports/mb/1mbo | HTTPS FTP |
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-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: INSPECTION OF MAPS AT VARIOUS STAGES OF REFINEMENT INDICATED THAT SEVERAL SIDE-CHAINS AND THE C- AND N-TERMINAL RESIDUES WERE DISORDERED TO SOME DEGREE. IN MOST CASES, ONE CONFORMATION WAS VERY ...1: INSPECTION OF MAPS AT VARIOUS STAGES OF REFINEMENT INDICATED THAT SEVERAL SIDE-CHAINS AND THE C- AND N-TERMINAL RESIDUES WERE DISORDERED TO SOME DEGREE. IN MOST CASES, ONE CONFORMATION WAS VERY MUCH STRONGER THAN THE OTHER, BUT FOUR SIDE-CHAINS WERE INCLUDED IN THE MODEL WITH TWO ALTERNATE CONFORMATIONS (VAL 13, LEU 86, LEU 89, GLN 128). 2: HOH 305 IS CLOSE TO ATOM O1 OF HEM 546. SEE PAPER CITED AS JRNL REFERENCE ABOVE. |
-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-SO4 / |
#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-OXY / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37.03 % |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.4 / Method: unknown |
-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Num. obs: 18494 / Num. measured all: 53607 / Rmerge(I) obs: 0.065 |
-Processing
Software | Name: CONSTRAINED / Version: RECIPROCAL-SPACE LEAST-SQUARES / Classification: refinement | ||||||||||||
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Refinement | Highest resolution: 1.6 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.6 Å
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Refinement | *PLUS Num. reflection obs: 18494 / σ(F): 3 / Rfactor all: 0.159 / Rfactor obs: 0.153 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |