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Yorodumi- PDB-6hav: Crystal structure of [Fe]-hydrogenase (Hmd) from Methanococcus ae... -
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-Basic information
Entry | Database: PDB / ID: 6hav | ||||||
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Title | Crystal structure of [Fe]-hydrogenase (Hmd) from Methanococcus aeolicus in complex with FeGP and methenyl-tetrahydromethanopterin (close form A) at 1.06 A resolution | ||||||
Components | 5,10-methenyltetrahydromethanopterin hydrogenase | ||||||
Keywords | OXIDOREDUCTASE / [Fe]-hydrogenase / catalytic cycle / conformational rearrangement / Fe-guanylylpyridinol cofactor / methanogenesis / hydride-transfer / tetrahydromethanopterin / C1-metabolism / atomic resolution | ||||||
Function / homology | Function and homology information 5,10-methenyltetrahydromethanopterin hydrogenase / N5,N10-methenyltetrahydromethanopterin hydrogenase activity / methanogenesis, from carbon dioxide / pyrroline-5-carboxylate reductase activity / L-proline biosynthetic process / one-carbon metabolic process Similarity search - Function | ||||||
Biological species | Methanococcus aeolicus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å | ||||||
Authors | Huang, G. / Wagner, T. / Wodrich, M.D. / Ataka, K. / Bill, E. / Ermler, U. / Hu, X. / Shima, S. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Catal / Year: 2019 Title: The atomic-resolution crystal structure of activated [Fe]-hydrogenase Authors: Huang, G. / Wagner, T. / Wodrich, M.D. / Ataka, K. / Bill, E. / Ermler, U. / Hu, X. / Shima, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hav.cif.gz | 173.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hav.ent.gz | 133.4 KB | Display | PDB format |
PDBx/mmJSON format | 6hav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hav_validation.pdf.gz | 926.9 KB | Display | wwPDB validaton report |
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Full document | 6hav_full_validation.pdf.gz | 935 KB | Display | |
Data in XML | 6hav_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 6hav_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/6hav ftp://data.pdbj.org/pub/pdb/validation_reports/ha/6hav | HTTPS FTP |
-Related structure data
Related structure data | 6hacSC 6haeC 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36784.562 Da / Num. of mol.: 1 / Mutation: wild type Source method: isolated from a genetically manipulated source Details: / Source: (gene. exp.) Methanococcus aeolicus (strain ATCC BAA-1280 / DSM 17508 / OCM 812 / Nankai-3) (archaea) Tissue: / / Cell: / / Cell line: / / Gene: hmd, Maeo_1025 / Organ: / / Variant: / / Plasmid: pET-24b+ / Details (production host): / / Cell (production host): / / Cell line (production host): / / Organ (production host): / / Production host: Escherichia coli BL21(DE3) (bacteria) / Tissue (production host): / / Variant (production host): / References: UniProt: A6UVT1, 5,10-methenyltetrahydromethanopterin hydrogenase |
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-Non-polymers , 6 types, 517 molecules
#2: Chemical | ChemComp-FE9 / | ||||||||
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#3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-E4M / | #7: 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: 2.52 Å3/Da / Density % sol: 51.17 % / Description: Large orthorhombic rod |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Crystallization of [Fe]-hydrogenase-methenyl-H4MPT+ complex was performed in the anaerobic tent with gas phase 100%N2 at room temperature under dark condition. The reconstituted [Fe]- ...Details: Crystallization of [Fe]-hydrogenase-methenyl-H4MPT+ complex was performed in the anaerobic tent with gas phase 100%N2 at room temperature under dark condition. The reconstituted [Fe]-hydrogenase holoenzyme (50 mg/ml) was mixed with 10 mM methenyl-H4MPT+, both of which contained 10 mM MOPS/KOH pH 7.0. The final concentrations of [Fe]-hydrogenase and methenyl-H4MPT+ were 24 mg/ml and 3 mM, respectively. After incubating the mixture in this tent under dark condition for 5 min, the enzyme solution was centrifuged at 8000 rpm for 5 min by using centrifugal filters made of polyvinylidene fluoride (PVDF, Millipore). The crystallization solution contained 20% w/v polyethylene glycol 3350 and 200 mM sodium thiocyanate with a ratio of protein mixture and crystallization reservoir of 2 ul / 2 ul drops spotted on a 24 well Junior Clover plate. The crystal was soaked for a couple of seconds in 20% w/v polyethylene glycol 3350, 20% v/v glycerol and 200 mM sodium thiocyanate before freezing in liquid nitrogen. PH range: / Temp details: Protein was crystallized at room temperature with + / - 4 degree |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 1.06→46.98 Å / Num. obs: 156432 / % possible obs: 93.7 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.021 / Rrim(I) all: 0.054 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.06→1.12 Å / Redundancy: 4 % / Rmerge(I) obs: 0.981 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 18054 / CC1/2: 0.672 / Rpim(I) all: 0.542 / Rrim(I) all: 1.129 / % possible all: 74.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6HAC Resolution: 1.06→45.24 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 12.41
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.06→45.24 Å
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Refine LS restraints |
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LS refinement shell |
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