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- PDB-6hux: HmdII from Methanocaldococcus jannaschii reconstitued with Fe-gua... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hux | |||||||||
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Title | HmdII from Methanocaldococcus jannaschii reconstitued with Fe-guanylylpyridinol (FeGP) cofactor and co-crystallized with methenyl-tetrahydromethanopterin at 2.5 A resolution | |||||||||
![]() | H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338 | |||||||||
![]() | OXIDOREDUCTASE / Hydrogenase / H2-activation / Lateral gene-transfer / cofactor biosynthesis / tetrahydromethanopterin / paralog / methanogen / metalloenzyme | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Watanabe, T. / Wagner, T. / Huang, G. / Kahnt, J. / Ataka, K. / Ermler, U. / Shima, S. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: The Bacterial [Fe]-Hydrogenase Paralog HmdII Uses Tetrahydrofolate Derivatives as Substrates. Authors: Watanabe, T. / Wagner, T. / Huang, G. / Kahnt, J. / Ataka, K. / Ermler, U. / Shima, 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 | ![]() | 165.5 KB | Display | ![]() |
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PDB format | ![]() | 130.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 965.1 KB | Display | ![]() |
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Full document | ![]() | 967.3 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6huyC ![]() 6huzC ![]() 4yt4S 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40663.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: / Source: (gene. exp.) ![]() ![]() Tissue: / / Cell: / / Cell line: / / Gene: MJ1338 / Organ: / / Details (production host): / / Cell (production host): / / Organ (production host): / / Production host: ![]() ![]() References: UniProt: Q58734, 5,10-methenyltetrahydromethanopterin hydrogenase |
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-Non-polymers , 9 types, 77 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/FE9.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/E4M.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE9.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/E4M.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-FE9 / | #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-E4M / | #6: Chemical | ChemComp-MG / | #7: Chemical | ChemComp-SO4 / #8: Chemical | #9: Chemical | ChemComp-CL / | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.25 % / Description: transparent flower shape |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: HmdII from Methanocaldococcus jannaschii reconstituted with Fe-guanylylpyridinol cofactor was cocrystallized with methenyl-tetrahydromethanopterin using the sitting drop vapor diffusion ...Details: HmdII from Methanocaldococcus jannaschii reconstituted with Fe-guanylylpyridinol cofactor was cocrystallized with methenyl-tetrahydromethanopterin using the sitting drop vapor diffusion method under N2/H2 (95%/5%) in red light condition. 20 mg/ml of reconstituted enzyme in 25 mM Tris pH 7.5, 5% glycerol, 150 mM NaCl, 2 mM DTT and 3 mM methenyl-tetrahydromethanopterin was spotted on a 96-well 2-drop MRC Crystallization Plates (Molecular Dimensions, Suffolk, UK) with a ratio of 0.7 ul of protein and 0.7 ul of reservoir solution. After several weeks, crystals appeared in 2 M LiSO4, 100 mM Sodium acetate pH 5.5, 100 mM MgSO4 and 5% v/v PEG 400. jHmdII crystal was cryoprotected in its mother liquor supplemented with 30% ethylene glycol before freezing in liquid nitrogen. Temp details: The temperature fluctuation was +/- 1 degree |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9799 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→43.73 Å / Num. obs: 15610 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 64.85 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.041 / Rrim(I) all: 0.129 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.341 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2224 / CC1/2: 0.686 / Rpim(I) all: 0.447 / Rrim(I) all: 1.415 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4YT4 Resolution: 2.5→38.97 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.912 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.372 / SU Rfree Blow DPI: 0.236 Details: The last refinement cycle was performed with hydrogens in riding position. The hydrogens have been removed from the deposited model.
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Displacement parameters | Biso mean: 64.84 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.5→38.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.67 Å / Total num. of bins used: 8
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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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