+Open data
-Basic information
Entry | Database: PDB / ID: 5d5r | ||||||
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Title | Horse-heart myoglobin - deoxy state | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE / myoglobin / heme protein | ||||||
Function / homology | Function and homology information nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding ...nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Barends, T. / Schlichting, I. | ||||||
Citation | Journal: Science / Year: 2015 Title: Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation. Authors: Barends, T.R. / Foucar, L. / Ardevol, A. / Nass, K. / Aquila, A. / Botha, S. / Doak, R.B. / Falahati, K. / Hartmann, E. / Hilpert, M. / Heinz, M. / Hoffmann, M.C. / Kofinger, J. / Koglin, J. ...Authors: Barends, T.R. / Foucar, L. / Ardevol, A. / Nass, K. / Aquila, A. / Botha, S. / Doak, R.B. / Falahati, K. / Hartmann, E. / Hilpert, M. / Heinz, M. / Hoffmann, M.C. / Kofinger, J. / Koglin, J.E. / Kovacsova, G. / Liang, M. / Milathianaki, D. / Lemke, H.T. / Reinstein, J. / Roome, C.M. / Shoeman, R.L. / Williams, G.J. / Burghardt, I. / Hummer, G. / Boutet, S. / Schlichting, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d5r.cif.gz | 47.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d5r.ent.gz | 32.3 KB | Display | PDB format |
PDBx/mmJSON format | 5d5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d5r_validation.pdf.gz | 798.6 KB | Display | wwPDB validaton report |
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Full document | 5d5r_full_validation.pdf.gz | 799.4 KB | Display | |
Data in XML | 5d5r_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 5d5r_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/5d5r ftp://data.pdbj.org/pub/pdb/validation_reports/d5/5d5r | HTTPS FTP |
-Related structure data
Related structure data | 5cmvSC 5cn4C 5cn5C 5cn6C 5cn7C 5cn8C 5cn9C 5cnbC 5cncC 5cndC 5cneC 5cnfC 5cngC 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: 16926.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P68082 |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 3.5 M ammonium sulphate, 0.1 M Tris-HCl pH 7.4 |
-Data collection
Diffraction | Mean temperature: 280 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→35 Å / Num. obs: 16486 / % possible obs: 96.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.9 / % possible all: 87.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CMV Resolution: 1.6→34.213 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→34.213 Å
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Refine LS restraints |
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LS refinement shell |
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