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- PDB-2w6y: Crystal structure of Sperm Whale Myoglobin mutant YQR in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2w6y | ||||||
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Title | Crystal structure of Sperm Whale Myoglobin mutant YQR in complex with Xenon | ||||||
![]() | MYOGLOBIN![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miele, A.E. / Draghi, F. / Renzi, F. / Sciara, G. / Johnson, K.A. / Vallone, B. / Brunori, M. / Savino, C. | ||||||
![]() | ![]() Title: When the Same Fold Does not Mean the Same Function: The Case of Xenon Cavities in Hemoglobin and Myoglobin Authors: Miele, A.E. / Draghi, F. / Johnson, K.A. / Renzi, F. / Sciara, G. / Brunori, M. / Vallone, B. / Savino, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.9 KB | Display | ![]() |
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PDB format | ![]() | 71.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 643.8 KB | Display | ![]() |
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Full document | ![]() | 644.9 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2w6xC ![]() 1nazS C: citing same article ( S: Starting model for refinement |
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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 on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 17462.234 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-HEM / ![]() | ||||||
#3: Chemical | ![]() #4: Chemical | ChemComp-XE / ![]() #5: Water | ChemComp-HOH / | ![]() Compound details | ENGINEERED RESIDUE IN CHAIN A, LEU 30 TO TYR ENGINEERED RESIDUE IN CHAIN A, HIS 65 TO GLN ...ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow![]() | pH: 8.7 / Details: 2.6M (NH4)2SO4, 0.1M TRIS/HCL, PH8.5, pH 8.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 6, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.6→26.1 Å / Num. obs: 28029 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.6→1.9 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1NAZ Resolution: 1.6→26 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.369 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.095 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.55 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→26 Å
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Refine LS restraints |
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