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Open data
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Basic information
Entry | Database: PDB / ID: 3.0E+55 | ||||||
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Title | Carbonmonoxy Sperm Whale Myoglobin at 100 K: Laser off | ||||||
![]() | Myoglobin![]() | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Tomita, A. / Sato, T. / Ichiyanagi, K. / Nozawa, S. / Ichikawa, H. / Chollet, M. / Kawai, F. / Park, S.-Y. / Koshihara, S. / Adachi, S. | ||||||
![]() | ![]() Title: Visualizing breathing motion of internal cavities in concert with ligand migration in myoglobin Authors: Tomita, A. / Sato, T. / Ichiyanagi, K. / Nozawa, S. / Ichikawa, H. / Chollet, M. / Kawai, F. / Park, S.-Y. / Tsuduki, T. / Yamato, T. / Koshihara, S.Y. / Adachi, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.9 KB | Display | ![]() |
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PDB format | ![]() | 62.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2zsnC ![]() 2zsoC ![]() 2zspC ![]() 2zsqC ![]() 2zsrC ![]() 2zssC ![]() 2zstC ![]() 2zsxC ![]() 2zsyC ![]() 2zszC ![]() 2zt0C ![]() 2zt1C ![]() 2zt2C ![]() 2zt3C ![]() 2zt4C ![]() 3e4nC ![]() 3e5iC ![]() 3e5oC ![]() 3eclC ![]() 3ecxC ![]() 3eczC ![]() 3ed9C ![]() 3edaC ![]() 3edbC ![]() 1mbcS S: Starting model for refinement C: citing same article ( |
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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
#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 | ![]() #3: Chemical | ChemComp-HEM / | ![]() #4: Chemical | ChemComp-CMO / | ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.19 % / Mosaicity: 0.377 ° |
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Crystal grow![]() | Temperature: 293 K / Method: batch / pH: 6 Details: 2.4M Ammonium sulfate, 10mM TrisHCl, 100mM Sodium phosphate, pH 6.0, batch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 19, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.21→50 Å / Num. obs: 37156 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.047 / Χ2: 0.832 / Net I/σ(I): 11.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1MBC Resolution: 1.21→14.97 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.148 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.891 / SU B: 1.471 / SU ML: 0.03 / SU R Cruickshank DPI: 0.049 / SU Rfree: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 45.15 Å2 / Biso mean: 15.421 Å2 / Biso min: 7.34 Å2
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Refinement step | Cycle: LAST / Resolution: 1.21→14.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.212→1.243 Å / Total num. of bins used: 20
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