+Open data
-Basic information
Entry | Database: PDB / ID: 2z6t | ||||||
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Title | Crystal structure of the ferric peroxo myoglobin | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN BINDING / X-ray-induced-photoreduction / peroxo / microspectrophotometer / Heme / Iron / Metal-binding / Muscle protein / Oxygen transport / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Unno, M. / Kusama, S. / Chen, H. / Shaik, S. / Ikeda-Saito, M. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2007 Title: Structural Characterization of the Fleeting Ferric Peroxo Species in Myoglobin: Experiment and Theory Authors: Unno, M. / Chen, H. / Kusama, S. / Shaik, S. / Ikeda-Saito, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z6t.cif.gz | 87.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z6t.ent.gz | 65.2 KB | Display | PDB format |
PDBx/mmJSON format | 2z6t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z6t_validation.pdf.gz | 808.2 KB | Display | wwPDB validaton report |
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Full document | 2z6t_full_validation.pdf.gz | 812.9 KB | Display | |
Data in XML | 2z6t_validation.xml.gz | 11 KB | Display | |
Data in CIF | 2z6t_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/2z6t ftp://data.pdbj.org/pub/pdb/validation_reports/z6/2z6t | HTTPS FTP |
-Related structure data
Related structure data | 2z6sSC S: Starting model for refinement C: citing same article (ref.) |
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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-PER / | #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: 1.88 Å3/Da / Density % sol: 34.49 % |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 6 Details: Ammonium Sulfate, pH6.0, LIQUID DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.6 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. all: 40287 / Num. obs: 39884 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.042 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.78 / Rsym value: 0.433 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Z6S Resolution: 1.2→8 Å / Cross valid method: Conjugated gradient / σ(F): 0 / σ(I): 0 / Stereochemistry target values: shelx
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Refinement step | Cycle: LAST / Resolution: 1.2→8 Å
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