+Open data
-Basic information
Entry | Database: PDB / ID: 8eac | ||||||
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Title | Thermus thermophilus methylenetetrahydrofolate reductase | ||||||
Components | Methylenetetrahydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / TIM barrel / flavin | ||||||
Function / homology | Function and homology information methylenetetrahydrofolate reductase (NADH) / methylenetetrahydrofolate reductase (NADH) activity / methionine biosynthetic process / tetrahydrofolate interconversion / nucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Yamada, K. / Koutmos, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: 5-Formyltetrahydrofolate promotes conformational remodeling in a methylenetetrahydrofolate reductase active site and inhibits its activity. Authors: Yamada, K. / Mendoza, J. / Koutmos, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8eac.cif.gz | 238.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8eac.ent.gz | 184.9 KB | Display | PDB format |
PDBx/mmJSON format | 8eac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/8eac ftp://data.pdbj.org/pub/pdb/validation_reports/ea/8eac | HTTPS FTP |
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-Related structure data
Related structure data | 7th4C 7th5C 3aptS S: Starting model for refinement 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
#1: Protein | Mass: 33050.887 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: ATCC 27634 / DSM 579 / HB8 / Gene: TTHA0327 / Production host: Escherichia coli (E. coli) References: UniProt: Q5SLG6, methylenetetrahydrofolate reductase [NAD(P)H] #2: Chemical | ChemComp-FAD / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.4 Å3/Da / Density % sol: 48.84 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion / pH: 7.8 / Details: 0.1M Hepes pH7.8, 1M LiCl, 20% PEG6k |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1271 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→89.06 Å / Num. obs: 49988 / % possible obs: 97.7 % / Redundancy: 6.5 % / CC1/2: 0.996 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.9→1.94 Å / Num. unique obs: 2948 / CC1/2: 0.965 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3apt Resolution: 1.9→80.734 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.585 / SU ML: 0.107 / Cross valid method: FREE R-VALUE / ESU R: 0.165 / ESU R Free: 0.155 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.143 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→80.734 Å
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Refine LS restraints |
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LS refinement shell |
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