+Open data
-Basic information
Entry | Database: PDB / ID: 1dxd | ||||||
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Title | Photolyzed CO complex of Myoglobin Mb-YQR at 20K | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN STORAGE / CO COMPLEX / RESPIRATORY PROTEIN | ||||||
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: 1.4 Å | ||||||
Authors | Brunori, M. / Vallone, B. / Cutruzzola, F. / Travaglini-Allocatelli, C. / Berendzen, J. / Chu, K. / Sweet, R.M. / Schlichting, I. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: The Role of Cavities in Protein Dynamics: Crystal Structure of a Photolytic Intermediate of a Mutant Myoglobin. Authors: Brunori, M. / Vallone, B. / Cutruzzola, F. / Travaglini-Allocatelli, C. / Berendzen, J. / Chu, K. / Sweet, R.M. / Schlichting, I. #1: Journal: Biophys.J. / Year: 1999 Title: Structural Dynamics of Liganddiffusion in the Protein Matrix: A Study on a New Myoglobin Mutant Y (B10) Q(E7) R(E10) Authors: Brunori, M. / Cutruzzola, F. / Savino, C. / Travaglini-Allocatelli, C. / Vallone, B. / Gibson, Q.H. #2: Journal: Nature / Year: 1994 Title: Crystal Structure of Photolysed Carbonmonoxy-Myoglobin Authors: Schlichting, I. / Berendzen, J. / Phillips Jr, G.N. / Sweet, R.M. #3: Journal: Proteins: Struct.,Funct., Genet. / Year: 1990 Title: Crystal Structure of Myoglobin from a Synthetic Gene Authors: Juniorarduini, R.M.G.N.P. / Springer, B.A. / Sligar, S.G. #4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987 Title: High-Level Expression of Sperm Whale Myoglobin in Escherichia Coli Authors: Springer, B.A. / Sligar, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dxd.cif.gz | 91.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dxd.ent.gz | 68.9 KB | Display | PDB format |
PDBx/mmJSON format | 1dxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dxd_validation.pdf.gz | 844.5 KB | Display | wwPDB validaton report |
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Full document | 1dxd_full_validation.pdf.gz | 847.7 KB | Display | |
Data in XML | 1dxd_validation.xml.gz | 12 KB | Display | |
Data in CIF | 1dxd_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/1dxd ftp://data.pdbj.org/pub/pdb/validation_reports/dx/1dxd | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | IN THIS SPACE GROUP THERE IS A STRONG 3 -FOLD CRYSTAL PACKINGOF THE MYOGLOBIN MOLECULE INVOLVING SYMMETRY OPERATIONS,(X,Y,Z), (1.0-X+ Y,1.0-X,Z), AND (1.0-Y,X-Y,Z). THE SO4MOLECULE 315 A SITS CLOSE TO THE 3-FOLD AXIS. |
-Components
#1: Protein | Mass: 17461.250 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: HEME BOUND TO HIS-93, CO IS PHOTODISSOCIATED FROM HEME IRON Source: (gene. exp.) PHYSETER CATODON (sperm whale) / Description: SYNTHETIC GENE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02185 | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | ChemComp-CMO / | ||
#4: Chemical | #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: 3.07 Å3/Da / Density % sol: 59.87 % | |||||||||||||||||||||||||
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Crystal grow | pH: 9 Details: PROTEIN WAS CRYSTALLIZED FROM 3.6 M AMMONIUM SULFATE.CRYSTALS WERE SOAKED FOR CA. 1 HOUR IN A THOROUGHLY DEGASSED AND CO SATURATED CRYOPROTECTANT SOLUTION MADE BY ADDITION OF 100 MG XYLITOL, ...Details: PROTEIN WAS CRYSTALLIZED FROM 3.6 M AMMONIUM SULFATE.CRYSTALS WERE SOAKED FOR CA. 1 HOUR IN A THOROUGHLY DEGASSED AND CO SATURATED CRYOPROTECTANT SOLUTION MADE BY ADDITION OF 100 MG XYLITOL, 100 MG GLUCOSE AND 8 MG NA-DITHIONATE TO 1 ML OF 70% SATURATED AMMONIUM SULFATE WITH 50 MM TRIS.HCL PH 9.0. DISTINCT COLOR CHANGES INDICATED THE FORMATION OF CO-MB FROM MET-MB. FOR PHOTOLYSIS PROTOCOL SEE REMARK 3. | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 8.7 / Method: vapor diffusionDetails: drop consists of equal volume of protein and reservoir solutions | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 20 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.91 |
Detector | Type: BRANDEIS / Detector: CCD / Date: May 15, 1998 / Details: MIRRORS |
Radiation | Monochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. obs: 41213 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 15.7 Å2 / Rsym value: 0.036 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.4→1.5 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.111 / % possible all: 99.1 |
Reflection | *PLUS Num. obs: 7686 / Num. measured all: 41213 / Rmerge(I) obs: 0.036 |
Reflection shell | *PLUS % possible obs: 99.1 % / Rmerge(I) obs: 0.111 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→18 Å / SU B: 0.63366 / SU ML: 0.02595 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04809 / ESU R Free: 0.04862
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Refinement step | Cycle: LAST / Resolution: 1.4→18 Å
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Refine LS restraints |
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