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Yorodumi- PDB-5ok4: Crystal structure of native [Fe]-hydrogenase Hmd from Methanother... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ok4 | ||||||
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Title | Crystal structure of native [Fe]-hydrogenase Hmd from Methanothermobacter marburgensis inactivated by O2. | ||||||
Components | 5,10-methenyltetrahydromethanopterin hydrogenase | ||||||
Keywords | OXIDOREDUCTASE / [Fe]-hydrogenase / Fe-Guanylylpyridinol cofactor / H2 / hydrogenase / methanogenesis / methenyl-tetrahydromethanopterin / methylene-tetrahydromethanopterin / hydrogenation / O2 / inactivation | ||||||
Function / homology | Function and homology information 5,10-methenyltetrahydromethanopterin hydrogenase / N5,N10-methenyltetrahydromethanopterin hydrogenase activity / methanogenesis, from carbon dioxide / one-carbon metabolic process Similarity search - Function | ||||||
Biological species | Methanothermobacter marburgensis str. Marburg (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å | ||||||
Authors | Wagner, T. / Huang, G. / Bill, E. / Ermler, U. / Ataka, K. / Shima, S. | ||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2018 Title: Dioxygen Sensitivity of [Fe]-Hydrogenase in the Presence of Reducing Substrates. Authors: Huang, G. / Wagner, T. / Ermler, U. / Bill, E. / Ataka, K. / Shima, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ok4.cif.gz | 164.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ok4.ent.gz | 128.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ok4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ok4_validation.pdf.gz | 761.7 KB | Display | wwPDB validaton report |
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Full document | 5ok4_full_validation.pdf.gz | 762.7 KB | Display | |
Data in XML | 5ok4_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 5ok4_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/5ok4 ftp://data.pdbj.org/pub/pdb/validation_reports/ok/5ok4 | HTTPS FTP |
-Related structure data
Related structure data | 2jjfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37692.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Methanothermobacter marburgensis str. Marburg (archaea) Cell line: / / Organ: / / Tissue: / References: UniProt: P32440, 5,10-methenyltetrahydromethanopterin hydrogenase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-FEG / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.04 % Description: Transparent cube shape of about 100x100 micrometer. |
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Crystal grow | Temperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1-ml mixture containing 120 mM potassium phosphate pH 6.0, 1 mM EDTA, 26 uM (1 mg/ml) [Fe]-hydrogenase and 26 uM methylene-H4MPT was incubated in 5-ml amber vials with rubber stoppers under ...Details: 1-ml mixture containing 120 mM potassium phosphate pH 6.0, 1 mM EDTA, 26 uM (1 mg/ml) [Fe]-hydrogenase and 26 uM methylene-H4MPT was incubated in 5-ml amber vials with rubber stoppers under a gas mixture of N2/O2/H2 (70%/20%/10%) at 40 degree Celsius for 1 h. The inactivated enzyme was concentrated to 25 mg/ml using a 30 kDa centrifugal filter (Millipore). 0.7-ul of 25 mg/ml O2-inactivated [Fe]-hydrogenase was mixed with 0.7 ul of reservoir solution of 2 M (NH4)2SO4, 100 mM Tris/HCl, pH 7.0, and 200 mM LiSO4. The best diffracting crystal was obtained in one month. Prior to freezing the crystal was soaked for 3 seconds in 2 M (NH4)2SO4, 100 mM Tris/HCl, pH 7.0, 200 mM LiSO4 and 30% glycerol v/v. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00005 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00005 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→47.07 Å / Num. obs: 110077 / % possible obs: 100 % / Redundancy: 8.2 % / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.018 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.29→1.36 Å / Redundancy: 8 % / Rmerge(I) obs: 1.128 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 15981 / CC1/2: 0.638 / Rpim(I) all: 0.423 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2JJF Resolution: 1.29→43.474 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.61
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.29→43.474 Å
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Refine LS restraints |
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LS refinement shell |
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