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- PDB-2ekt: Crystal structure of myoglobin reconstituted with 6-methyl-6-depr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ekt | ||||||
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Title | Crystal structure of myoglobin reconstituted with 6-methyl-6-depropionatehemin | ||||||
![]() | Myoglobin![]() | ||||||
![]() | OXYGEN STORAGE/TRANSPORT / ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Harada, K. / Makino, M. / Sugimoto, H. / Hirota, S. / Matsuo, T. / Shiro, Y. / Hisaeda, Y. / Hayashi, T. | ||||||
![]() | ![]() Title: Structure and ligand binding properties of myoglobins reconstituted with monodepropionated heme: functional role of each heme propionate side chain Authors: Harada, K. / Makino, M. / Sugimoto, H. / Hirota, S. / Matsuo, T. / Shiro, Y. / Hisaeda, Y. / Hayashi, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.6 KB | Display | ![]() |
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PDB format | ![]() | 71 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 626.1 KB | Display | ![]() |
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Full document | ![]() | 628.4 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ekuC ![]() 1jw8S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 17234.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-SO4 / ![]() #3: Chemical | ChemComp-6HE / | #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.22 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 3.0M ammonium sulfate, 100mM bis-tris propane, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 18, 2004 |
Radiation | Monochromator: SI(III) MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.1→50 Å / Num. obs: 85421 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 23.5 % / Rsym value: 0.062 / Net I/σ(I): 38.7 |
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 14.6 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 8466 / Rsym value: 0.349 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1JW8 Resolution: 1.1→10 Å / Num. parameters: 14631 / Num. restraintsaints: 17821 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 1095 / Occupancy sum non hydrogen: 1577.33 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→10 Å
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Refine LS restraints |
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