+Open data
-Basic information
Entry | Database: PDB / ID: 2zss | ||||||
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Title | Carbonmonoxy Sperm Whale Myoglobin at 140 K: Laser on [300 min] | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / haem protein / myoglobin / ligand migration / photodissociation | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.21 Å | ||||||
Authors | Tomita, A. / Sato, T. / Ichiyanagi, K. / Nozawa, S. / Ichikawa, H. / Chollet, M. / Kawai, F. / Park, S.-Y. / Koshihara, S. / Adachi, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 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. / Adachi, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zss.cif.gz | 84.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zss.ent.gz | 61.8 KB | Display | PDB format |
PDBx/mmJSON format | 2zss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/2zss ftp://data.pdbj.org/pub/pdb/validation_reports/zs/2zss | HTTPS FTP |
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-Related structure data
Related structure data | 2zsnC 2zsoC 2zspC 2zsqC 2zsrC 2zstC 2zsxC 2zsyC 2zszC 2zt0C 2zt1C 2zt2C 2zt3C 2zt4C 3e4nC 3e55C 3e5iC 3e5oC 3eclC 3ecxC 3eczC 3ed9C 3edaC 3edbC 1mbcS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-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 natural source / Source: (natural) Physeter catodon (sperm whale) / References: UniProt: P02185 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Chemical | ChemComp-CMO / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.38 % / Mosaicity: 0.603 ° |
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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: 140 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW14A / Wavelength: 0.827 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 21, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.827 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.21→50 Å / Num. obs: 33117 / % possible obs: 83.5 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.053 / Χ2: 0.756 / Net I/σ(I): 8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MBC Resolution: 1.21→17.02 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.203 / WRfactor Rwork: 0.147 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.821 / SU B: 2.392 / SU ML: 0.045 / SU R Cruickshank DPI: 0.057 / SU Rfree: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.06 / 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: 45.23 Å2 / Biso mean: 16.194 Å2 / Biso min: 7.07 Å2
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Refinement step | Cycle: LAST / Resolution: 1.21→17.02 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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