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Open data
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Basic information
Entry | Database: PDB / ID: 1cik | ||||||
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Title | RECOMBINANT SPERM WHALE MYOGLOBIN I99A MUTANT (MET) | ||||||
![]() | PROTEIN (MYOGLOBIN) | ||||||
![]() | OXYGEN STORAGE/TRANSPORT / OXYGEN TRANSPORT / HEME / MUSCLE PROTEIN / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Liong, E.C. / Phillips Jr., G.N. | ||||||
![]() | ![]() Title: Waterproofing the heme pocket. Role of proximal amino acid side chains in preventing hemin loss from myoglobin. Authors: Liong, E.C. / Dou, Y. / Scott, E.E. / Olson, J.S. / Phillips Jr., G.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.9 KB | Display | ![]() |
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PDB format | ![]() | 33.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ch1C ![]() 1ch2C ![]() 1ch3C ![]() 1ch5C ![]() 1ch7C ![]() 1ch9C ![]() 1cioC ![]() 1co8C ![]() 1co9C ![]() 1cp0C ![]() 1cp5C ![]() 1cpwC ![]() 1dtiC ![]() 1mbw S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17323.084 Da / Num. of mol.: 1 / Mutation: INITIATOR MET, I99A, D122N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 61.61 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 9 / Details: 2.6-3.0 M (NH4)2SO4, 20 MM TRIS, 1 MM EDTA, PH 9.0 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 9 / PH range high: 8 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 26136 / Num. obs: 26136 / % possible obs: 92.5 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.037 |
Reflection | *PLUS Num. obs: 22498 / Num. measured all: 67688 |
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Processing
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 1MBW ![]() 1mbw Resolution: 1.7→5 Å / Num. parameters: 5784 / Num. restraintsaints: 5420 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1445.3 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→5 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.186 / Rfactor Rwork: 0.156 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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