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Open data
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Basic information
Entry | Database: PDB / ID: 1duk | ||||||
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Title | WILD-TYPE RECOMBINANT SPERM WHALE METAQUOMYOGLOBIN | ||||||
![]() | WILD-TYPE RECOMBINANT SPERM WHALE METAQUOMYOGLOBIN | ||||||
![]() | OXYGEN STORAGE/TRANSPORT / Oxygen-storage protein / myoglobin / heme 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 | ![]() | ||||||
![]() | Barrick, D. / Dahlquist, F.W. | ||||||
![]() | ![]() Title: Trans-substitution of the proximal hydrogen bond in myoglobin: I. Structural consequences of hydrogen bond deletion. Authors: Barrick, D. / Dahlquist, F.W. #1: ![]() Title: Trans-substitution of the proximal hydrogen bond in myoglobin: II. Energetics, functional consequences, and implications for hemoglobin allostery Authors: Barrick, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44 KB | Display | ![]() |
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PDB format | ![]() | 30.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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: 17234.951 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: FERRIC PROTOPORPHYRIN IX BOUND DURING BACTERIAL EXPRESSION OF THE PROTEIN Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.72 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop Details: 35 % PEG 8000, 0.3 M NaOAc, 0.1 M PIPES, VAPOR DIFFUSION, HANGING DROP Temp details: Room temperature | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 Details: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Ambient temp details: Room temperature |
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Diffraction source | Source: ![]() |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Feb 11, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→20 Å / Num. all: 7405 / Num. obs: 7405 / % possible obs: 78 % / Redundancy: 2.21 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 7.74 |
Reflection shell | Resolution: 2.13→2.29 Å / Redundancy: 1.36 % / Rmerge(I) obs: 0.163 / Num. unique all: 838 / % possible all: 47 |
Reflection shell | *PLUS % possible obs: 47 % |
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Processing
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Refinement | Resolution: 2.13→20 Å Stereochemistry target values: Bond lengths 0.02 rms; bond angles 3 degrees rms, trig planes 0.02 rms; general planes 0.02 rms; B-correlation 6.0 square angstroms rms.
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Refinement step | Cycle: LAST / Resolution: 2.13→20 Å
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Refine LS restraints |
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