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- PDB-6ykb: [Fe]-hydrogenase from Methanolacinia paynteri in complex with GMP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ykb | ||||||||||||
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Title | [Fe]-hydrogenase from Methanolacinia paynteri in complex with GMP at 1.55-A resolution | ||||||||||||
![]() | 5,10-methenyltetrahydromethanopterin [Fe]-hydrogenase | ||||||||||||
![]() | OXIDOREDUCTASE / [Fe]-hydrogenase / FeGP cofactor / guanylylpyridinol / conformational changes / GMP | ||||||||||||
Function / homology | GUANOSINE-5'-MONOPHOSPHATE / FORMIC ACID![]() | ||||||||||||
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 | ![]() | 286.4 KB | Display | ![]() |
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PDB format | ![]() | 229.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 32 KB | Display | |
Data in CIF | ![]() | 48.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tgeC ![]() 6tlkC ![]() 6tm3C ![]() 6yk9C ![]() 6ykaC ![]() 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
#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: / / Variant: DSM 2545 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: 5,10-methenyltetrahydromethanopterin hydrogenase #2: Chemical | #3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-GOL / | #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: 2.36 Å3/Da / Density % sol: 47.95 % / Description: Large rod shape |
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Crystal grow | Temperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Fe-hydrogenase holoenzyme from Methanolacinia paynteri was crystallized under 95%N2/5%H2 at 8 degree Celsius using a 96-well two-drop MRC crystallization plates. 0.7 ul of 25 mg/ml ...Details: Fe-hydrogenase holoenzyme from Methanolacinia paynteri was crystallized under 95%N2/5%H2 at 8 degree Celsius using a 96-well two-drop MRC crystallization plates. 0.7 ul of 25 mg/ml reconstituted enzyme with an Fe(II)-complex mimicking the FeGP cofactor and GMP (2mM final) was mixed with 0.7-ul reservoir solution under yellow light and incubated under dark conditions. The best crystal appeared within one month in 20% w/v polyethylene glycol 3350 and 200-mM magnesium formate reservoir solution (JBScreen Wizard 3&4 HTS, Jena Bioscience). The cryo protection was performed by adding 30% glycerol final to the crystallization solution. PH range: 7 / 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: 0.97972 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→95.095 Å / Num. obs: 104812 / % possible obs: 99.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 16.43 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.041 / Rrim(I) all: 0.08 / Rsym value: 0.068 / Net I/av σ(I): 8.8 / Net I/σ(I): 12.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JJF Resolution: 1.55→22.69 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.081 / SU Rfree Blow DPI: 0.079 / SU Rfree Cruickshank DPI: 0.077
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Displacement parameters | Biso max: 110.92 Å2 / Biso mean: 22.16 Å2 / Biso min: 3.28 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→22.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 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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