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- PDB-6yka: Asymmetric [Fe]-hydrogenase from Methanolacinia paynteri apo and ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6yka | ||||||||||||
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Title | Asymmetric [Fe]-hydrogenase from Methanolacinia paynteri apo and in complex with FeGP at 2.1-A resolution | ||||||||||||
![]() | 5,10-methenyltetrahydromethanopterin hydrogenase![]() | ||||||||||||
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Function / homology | iron-guanylyl pyridinol cofactor / ![]() ![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Wagner, T. / Huang, G. / Arriaza-Gallardo, F.J. / Shima, S. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: The Hydride Transfer Process in NADP-dependent Methylene-tetrahydromethanopterin Dehydrogenase. Authors: Huang, G. / Wagner, T. / Demmer, U. / Warkentin, E. / 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 | ![]() | 285.5 KB | Display | ![]() |
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PDB format | ![]() | 231.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6tgeC ![]() 6tlkC ![]() 6tm3C ![]() 6yk9C ![]() 6ykbC ![]() 4jjfS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | ![]() Mass: 37223.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: / Source: (gene. exp.) ![]() ![]() Tissue: / / Cell: / / Cell line: / / Gene: hmd / Organ: / Details (production host): The DNA synthesized was inserted into the expression vector pET-24b (+) at the NdeI and SalI restriction-enzyme digestion-sites Cell (production host): / / Organ (production host): / / Production host: ![]() ![]() ![]() References: ![]() |
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-Non-polymers , 5 types, 236 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FE9.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FE9.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / ![]() #3: Chemical | ![]() #4: Chemical | ![]() #5: Chemical | ChemComp-FE9 / | #6: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.45 % / Description: Transparent prism shape |
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Crystal grow![]() | Temperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: [Fe]-hydrogenase holoenzyme from M. paynteri was crystallized under 95%N2/5%H2 using 96-well two-drop MRC crystallization plates (sitting drop vapor diffusion method). 0.7 ul of 25-mg/ml ...Details: [Fe]-hydrogenase holoenzyme from M. paynteri was crystallized under 95%N2/5%H2 using 96-well two-drop MRC crystallization plates (sitting drop vapor diffusion method). 0.7 ul of 25-mg/ml reconstituted holoenzyme was mixed with 0.7-ul reservoir solution under yellow light and incubated under dark conditions. The crystals grew within two weeks in 30% w/v polyethylene glycol 4000, 200-mM lithium sulfate and 100-mM Tris pH 8.5 (JBScreen Wizard 3&4 HTS, Jena Bioscience). PH range: 8.5 / Temp details: / |
-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: Sep 23, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→68.833 Å / Num. obs: 39181 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 41.7 Å2 / CC1/2: 1 / Rpim(I) all: 0.019 / Rrim(I) all: 0.062 / Rsym value: 0.059 / Net I/av σ(I): 11.7 / Net I/σ(I): 28.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4JJF Resolution: 2.1→39.74 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.241 / SU Rfree Blow DPI: 0.186
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Displacement parameters | Biso max: 220.76 Å2 / Biso mean: 61.86 Å2 / Biso min: 15.59 Å2
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Refine analyze | Luzzati coordinate error obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→39.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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