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Yorodumi- PDB-1do7: CARBONMONOXY-MYOGLOBIN (MUTANT L29W) REBINDING STRUCTURE AFTER PH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1do7 | |||||||||
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Title | CARBONMONOXY-MYOGLOBIN (MUTANT L29W) REBINDING STRUCTURE AFTER PHOTOLYSIS AT T< 180K | |||||||||
Components | MYOGLOBIN | |||||||||
Keywords | OXYGEN STORAGE/TRANSPORT / HEME / RESPIRATORY PROTEIN / PHOTOLYSED MYOGLOBIN / LIGAND MIGRATION / OXYGEN STORAGE-TRANSPORT COMPLEX | |||||||||
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 / Resolution: 1.85 Å | |||||||||
Authors | Ostermann, A. / Waschipky, R. / Parak, F.G. / Nienhaus, G.U. | |||||||||
Citation | Journal: Nature / Year: 2000 Title: Ligand binding and conformational motions in myoglobin. Authors: Ostermann, A. / Waschipky, R. / Parak, F.G. / Nienhaus, G.U. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1do7.cif.gz | 53.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1do7.ent.gz | 35.1 KB | Display | PDB format |
PDBx/mmJSON format | 1do7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1do7_validation.pdf.gz | 524.9 KB | Display | wwPDB validaton report |
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Full document | 1do7_full_validation.pdf.gz | 523.9 KB | Display | |
Data in XML | 1do7_validation.xml.gz | 5 KB | Display | |
Data in CIF | 1do7_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/1do7 ftp://data.pdbj.org/pub/pdb/validation_reports/do/1do7 | HTTPS FTP |
-Related structure data
Related structure data | 1do1C 1do3C 1do4SC 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 on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 17466.225 Da / Num. of mol.: 1 / Mutation: M0(FME), L29W, D122N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Production host: Escherichia coli (E. coli) / References: UniProt: P02185 |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose |
-Non-polymers , 4 types, 190 molecules
#3: Chemical | #4: Chemical | ChemComp-HEM / | #5: Chemical | ChemComp-CMO / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.76 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: batch crystallization / pH: 8.5 Details: CRYSTALS WERE GROWN IN 2.5M AMMONIUM SULFATE SOLUTION, BUFFERED WITH 20MM TRIS/ HCL TO PH 8.5. THE CRYSTALLIZATION SOLUTION WAS REPLACED IN STEPS AGAINST A SOLUTION CONTAINING 2.5M AMMONIUM ...Details: CRYSTALS WERE GROWN IN 2.5M AMMONIUM SULFATE SOLUTION, BUFFERED WITH 20MM TRIS/ HCL TO PH 8.5. THE CRYSTALLIZATION SOLUTION WAS REPLACED IN STEPS AGAINST A SOLUTION CONTAINING 2.5M AMMONIUM SULFATE, 20MM TRIS, 300MG/ML TREHALOSE AT PH 8.5., BATCH CRYSTALLIZATION, temperature 292K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: unknown | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54 |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Nov 20, 1998 / Details: graphite |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→7 Å / Num. obs: 16415 / % possible obs: 90.3 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 8.9 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.85→1.91 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 5.5 / % possible all: 76.7 |
Reflection | *PLUS Num. measured all: 108921 |
Reflection shell | *PLUS % possible obs: 76.7 % |
-Processing
Software |
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Refinement | Starting model: 1do4 Resolution: 1.85→7 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: free r / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: NO ANGLE RESTRAINTS WERE USED FOR THE CO MOLECULE AND THE HIS 93 WITH RESPECT TO THE IRON ATOM. BOND RESTRAINTS FOR THE CO MOLECULE, HIS 93 AND FOR THE 4 PYRROLE NITROGEN TO THE IRON ATOM ...Details: NO ANGLE RESTRAINTS WERE USED FOR THE CO MOLECULE AND THE HIS 93 WITH RESPECT TO THE IRON ATOM. BOND RESTRAINTS FOR THE CO MOLECULE, HIS 93 AND FOR THE 4 PYRROLE NITROGEN TO THE IRON ATOM WERE WEAKENED FROM THE STANDARD X-PLOR VALUES (PARAM19X.HEME). THERE IS NEARLY NO ELECTRON DENSITY FOR THE N-FORMYL-MET. THIS RESIDUE WAS NOT INCLUDED INTO THE MODEL. ELECTRON DENSITY FEATURES CLOSE TO THIS SITE WERE MODELED BY WATER MOLECULES. ONE TREHALOSE MOLECULE IS BOUND TO THE SURFACE OF THE MYOGLOBIN MOLECULE. THE WATER MOLECULES NUMBER 246 AND 252 ARE ON OR CLOSE TO SPECIAL POSITIONS.
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Refine analyze | Luzzati d res low obs: 7 Å / Luzzati sigma a obs: 0.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.93 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 7 Å / σ(F): 0 / Rfactor obs: 0.186 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.253 / Rfactor Rwork: 0.221 |