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- PDB-7dih: Crystal structure of Thermoglobin Y29F mutant in complex with imi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dih | ||||||
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Title | Crystal structure of Thermoglobin Y29F mutant in complex with imidazole | ||||||
![]() | Thermoglobin | ||||||
![]() | OXYGEN BINDING / hemoglobin / monomer | ||||||
Function / homology | ![]() nitric oxide dioxygenase NAD(P)H activity / cellular response to nitrosative stress / nitric oxide catabolic process / FAD binding / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Muraki, N. / Aono, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Characterization of Y29F Mutant of Thermoglobin from a Hyperthermophilic Bacterium Aquifex aeolicus Authors: Muraki, N. / Takeda, K. / Nam, D. / Muraki, M. / Aono, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.7 KB | Display | ![]() |
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PDB format | ![]() | 99.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 16.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1vhbS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16252.726 Da / Num. of mol.: 2 / Mutation: Y29F Source method: isolated from a genetically manipulated source Details: N-terminal three amino acids (GSH) is a part of expression tag, which was digested by protease. Source: (gene. exp.) ![]() ![]() Strain: VF5 / Gene: aq_211 / Plasmid: pET15b / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.69 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 3.0 M ammonium sulfide, 0.1 M sodium cacodylate pH 6.0, 2 % PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→38.03 Å / Num. obs: 46830 / % possible obs: 99.5 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.024 / Rrim(I) all: 0.046 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2116 / Rpim(I) all: 0.501 / Rrim(I) all: 0.807 / % possible all: 93.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1vhb Resolution: 1.5→38.022 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→38.022 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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