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Yorodumi- PDB-5odh: Heterodisulfide reductase / [NiFe]-hydrogenase complex from Metha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5odh | ||||||
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Title | Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus soaked with heterodisulfide for 3.5 minutes | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Heterodisulfide reductase / [NiFe]-hydrogenase / FeS cluster / ferredoxin / CCG motif / methanogenesis / flavoprotein / flavin-based electron bifurcation / [2Fe-2S] cluster / macromolecular complex / anaerobic / thioredoxin / metabolism | ||||||
Function / homology | Function and homology information dihydromethanophenazine:CoB-CoM heterodisulfide reductase / hydrogen dehydrogenase / hydrogen dehydrogenase activity / CoB--CoM heterodisulfide reductase activity / Oxidoreductases; Acting on a sulfur group of donors / hydrogenase (acceptor) / methanogenesis / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / iron-sulfur cluster binding ...dihydromethanophenazine:CoB-CoM heterodisulfide reductase / hydrogen dehydrogenase / hydrogen dehydrogenase activity / CoB--CoM heterodisulfide reductase activity / Oxidoreductases; Acting on a sulfur group of donors / hydrogenase (acceptor) / methanogenesis / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / iron-sulfur cluster binding / nickel cation binding / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Methanothermococcus thermolithotrophicus DSM 2095 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Wagner, T. / Koch, J. / Ermler, U. / Shima, S. | ||||||
Citation | Journal: Science / Year: 2017 Title: Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction. Authors: Wagner, T. / Koch, J. / Ermler, U. / Shima, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5odh.cif.gz | 815.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5odh.ent.gz | 655.5 KB | Display | PDB format |
PDBx/mmJSON format | 5odh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/5odh ftp://data.pdbj.org/pub/pdb/validation_reports/od/5odh | HTTPS FTP |
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-Related structure data
Related structure data | 5odcSC 5odiC 5odqC 5odrC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Heterodisulfide reductase, subunit ... , 3 types, 6 molecules AGBHCI
#1: Protein | Mass: 71591.672 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea) Cell line: / / Organ: / / Variant: / / Tissue: / / References: UniProt: A0A2D0TCB9*PLUS #2: Protein | Mass: 32075.318 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source Details: This subunit contains two pentacoordinated non cubane [4Fe-4S] clusters Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea) Cell line: / / Organ: / / Variant: / / Tissue: / References: UniProt: A0A2D0TCB4*PLUS, dihydromethanophenazine:CoB-CoM heterodisulfide reductase #3: Protein | Mass: 20483.650 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea) Cell line: / / Organ: / / Variant: / / Tissue: / / References: UniProt: A0A2D0TC97*PLUS |
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-Methyl-viologen reducing hydrogenase, subunit ... , 3 types, 6 molecules DJEKFL
#4: Protein | Mass: 16057.495 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea) Cell line: / / Organ: / / Variant: / / Tissue: / / References: UniProt: A0A2D0TC98*PLUS #5: Protein | Mass: 32511.432 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea) Cell line: / / Organ: / / Variant: / / Tissue: / References: UniProt: A0A2D0TC99*PLUS, hydrogen dehydrogenase #6: Protein | Mass: 53129.602 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source Details: The C-terminus has been already post-translationally cleaved Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea) Cell line: / / Organ: / / Variant: / / Tissue: / References: UniProt: A0A2D0TCA6*PLUS, hydrogen dehydrogenase |
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-Non-polymers , 13 types, 661 molecules
#7: Chemical | ChemComp-SF4 / #8: Chemical | ChemComp-GOL / #9: Chemical | ChemComp-PE3 / #10: Chemical | #11: Chemical | ChemComp-9S8 / #12: Chemical | #13: Chemical | #14: Chemical | ChemComp-TRS / | #15: Chemical | #16: Chemical | #17: Chemical | #18: Chemical | ChemComp-TP7 / | #19: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.5 % Description: Black thick plate square shape of about 0.2-0.4 mm |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: All crystallization was performed in an anaerobic chamber (95% N2/5% H2) with anoxic solution using the sitting drop method (96-well 2-drop MRC Crystallization Plates in polystyrene, ...Details: All crystallization was performed in an anaerobic chamber (95% N2/5% H2) with anoxic solution using the sitting drop method (96-well 2-drop MRC Crystallization Plates in polystyrene, Molecular Dimensions, Suffolk, UK). The crystallization reservoir contained 100 mM Tris/HCl, pH 8.5, 3% (v/v) DMSO, 30% (w/v) polyethylene glycol 4000, and 200 mM Na acetate trihydrate. Crystallization drop contained 1 ul HdrABC-MvhAGD at 25 mg/ml premixed with 2 mM FAD and 1 ul of precipitant. The crystals appeared after 1-2 weeks in this condition. The cryo-cool trapping experiment was performed as following: crystals were soaked for 3min30sec in the crystallization solution supplemented with 66 mM CoM-S-S-CoB. The crystal was cryo-protected by a soak in the crystallization solution supplemented by 30% glycerol and 10 mM CoM-S-S-CoB. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97916 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→48.552 Å / Num. obs: 225651 / % possible obs: 99.8 % / Redundancy: 4.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.073 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.435 / Num. unique obs: 32668 / CC1/2: 0.451 / Rpim(I) all: 0.237 / % possible all: 99.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ODC Resolution: 2.2→48.552 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.47
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→48.552 Å
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Refine LS restraints |
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LS refinement shell |
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