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Open data
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Basic information
Entry | Database: PDB / ID: 5v8s | ||||||
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Title | Flavo di-iron protein H90D mutant from Thermotoga maritima | ||||||
![]() | Flavoprotein | ||||||
![]() | ELECTRON TRANSPORT / TM0755 / FLAVOPROTEIN / DI-IRON PROTEIN | ||||||
Function / homology | ![]() FMN binding / oxidoreductase activity / electron transfer activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Taylor, A.B. / Becker, A. / Giri, N. / Hart, P.J. / Kurtz Jr., D.M. | ||||||
![]() | ![]() Title: Flavo Di-iron protein H90D Mutant from Thermotoga Maritima Authors: Kurtz Jr., D.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 343.7 KB | Display | ![]() |
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PDB format | ![]() | 278 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.8 KB | Display | ![]() |
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Full document | ![]() | 478.7 KB | Display | |
Data in XML | ![]() | 33.5 KB | Display | |
Data in CIF | ![]() | 49.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dilS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46771.680 Da / Num. of mol.: 2 / Mutation: H90D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0755, Tmari_0756 / Plasmid: pMH1 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 524 molecules ![](data/chem/img/FEO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.02 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M SODIUM ACETATE, 45% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→84.98 Å / Num. obs: 158720 / % possible obs: 98.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 18 Å2 / Rpim(I) all: 0.03 / Rsym value: 0.058 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.41→1.49 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2 / Num. unique obs: 23232 / Rpim(I) all: 0.345 / Rsym value: 0.659 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DIL Resolution: 1.41→84.98 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 21.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.41→84.98 Å
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Refine LS restraints |
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LS refinement shell |
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