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Yorodumi- PDB-8qpm: Structure of methylene-tetrahydromethanopterin reductase from Met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qpm | ||||||
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Title | Structure of methylene-tetrahydromethanopterin reductase from Methanocaldococcus jannaschii | ||||||
Components | 5,10-methylenetetrahydromethanopterin reductase | ||||||
Keywords | OXIDOREDUCTASE / methylene-tetrahydropterin reductase | ||||||
Function / homology | Function and homology information 5,10-methylenetetrahydromethanopterin reductase / coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase activity / methanogenesis, from carbon dioxide / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / one-carbon metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Gehl, M. / Demmer, U. / Ermler, U. / Shima, S. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Protein Sci. / Year: 2024 Title: Mutational and structural studies of ( beta alpha ) 8 -barrel fold methylene-tetrahydropterin reductases utilizing a common catalytic mechanism. Authors: Gehl, M. / Demmer, U. / 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 | 8qpm.cif.gz | 723.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qpm.ent.gz | 616.5 KB | Display | PDB format |
PDBx/mmJSON format | 8qpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qpm_validation.pdf.gz | 450.5 KB | Display | wwPDB validaton report |
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Full document | 8qpm_full_validation.pdf.gz | 463.5 KB | Display | |
Data in XML | 8qpm_validation.xml.gz | 51.1 KB | Display | |
Data in CIF | 8qpm_validation.cif.gz | 74.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/8qpm ftp://data.pdbj.org/pub/pdb/validation_reports/qp/8qpm | HTTPS FTP |
-Related structure data
Related structure data | 8qpjC 8qplC 8qq8C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35836.656 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: mer, HA335_01095 / Production host: Escherichia coli (E. coli) References: UniProt: A0A832SYB5, 5,10-methylenetetrahydromethanopterin reductase #2: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.74 Å3/Da / Density % sol: 55.12 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop Details: 35% (v/v) 2-methyl-2,4-pentanediol, 100 mM sodium acetate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48.33 Å / Num. obs: 144127 / % possible obs: 99.84 % / Redundancy: 3.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.109 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.8→1.864 Å / Rmerge(I) obs: 0.822 / Num. unique obs: 14203 / CC1/2: 0.503 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.33 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.8→48.33 Å
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