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Open data
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Basic information
Entry | Database: PDB / ID: 7dds | |||||||||
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Title | Ancestral myoglobin aMbSp of Puijila Darwini relative | |||||||||
![]() | Ancestral myoglobin aMbSp | |||||||||
![]() | OXYGEN STORAGE / Protein evolution / Ancestral protein / Diving adaptation / Seals | |||||||||
Function / homology | PROTOPORPHYRIN IX CONTAINING FE![]() | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Isogai, Y. / Imamura, H. / Nakae, S. / Sumi, T. / Takahashi, K. / Shirai, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Common and unique strategies of myoglobin evolution for deep-sea adaptation of diving mammals. Authors: Isogai, Y. / Imamura, H. / Nakae, S. / Sumi, T. / Takahashi, K.I. / Shirai, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.5 KB | Display | ![]() |
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PDB format | ![]() | 54.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 785.8 KB | Display | ![]() |
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Full document | ![]() | 786.5 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 11.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ddrC ![]() 7ddtC ![]() 7dduC ![]() 5yceS 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: 17156.768 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.11 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.6M tri-Sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: May 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 6494 / % possible obs: 99.7 % / Redundancy: 2 % / Biso Wilson estimate: 23.78 Å2 / Rmerge(I) obs: 0.024 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.3→2.42 Å / Rmerge(I) obs: 0.037 / Num. unique obs: 930 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5YCE Resolution: 2.3→20 Å / SU ML: 0.2996 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 22.8454 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.63 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell |
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