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Yorodumi- PDB-8qq8: Crystal Structure of F420-dependent Methylene-Tetrahydromethanopt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qq8 | ||||||
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Title | Crystal Structure of F420-dependent Methylene-Tetrahydromethanopterin Reductase Mutant E6Q from Methanocaldococcus Jannaschii | ||||||
Components | 5,10-methylenetetrahydromethanopterin reductase | ||||||
Keywords | OXIDOREDUCTASE / F420-dependent methylene-tetrahydromethanopterin 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: 2 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 | 8qq8.cif.gz | 144.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qq8.ent.gz | 112.1 KB | Display | PDB format |
PDBx/mmJSON format | 8qq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qq8_validation.pdf.gz | 423.6 KB | Display | wwPDB validaton report |
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Full document | 8qq8_full_validation.pdf.gz | 427.5 KB | Display | |
Data in XML | 8qq8_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 8qq8_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/8qq8 ftp://data.pdbj.org/pub/pdb/validation_reports/qq/8qq8 | HTTPS FTP |
-Related structure data
Related structure data | 8qpjC 8qplC 8qpmC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 35393.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: mer / Production host: Escherichia coli (E. coli) / References: UniProt: A0A832SYB5 |
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#2: 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: 3.41 Å3/Da / Density % sol: 63.88 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop Details: 15 % w/v Polyethylene glycol 4,000 200 mM Ammonium sulfate 2 mM F420 2 mM CH3-H4MPT 20 mg/ml jMer_E6Q |
-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 EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→40.65 Å / Num. obs: 33460 / % possible obs: 99.2 % / Redundancy: 4.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.23 |
Reflection shell | Resolution: 2→2.1 Å / Rmerge(I) obs: 1.9 / Num. unique obs: 4452 / CC1/2: 0.491 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40.65 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→40.65 Å
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Refine LS restraints |
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LS refinement shell |
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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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