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Yorodumi- PDB-3apt: properties and crystal structure of methylenetetrahydrofolate red... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3apt | ||||||
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Title | properties and crystal structure of methylenetetrahydrofolate reductase from Thermus thermophilus HB8 | ||||||
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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Yamada, K. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Properties and Crystal Structure of Methylenetetrahydrofolate Reductase from Thermus thermophilus HB8. Authors: Igari, S. / Ohtaki, A. / Yamanaka, Y. / Sato, Y. / Yohda, M. / Odaka, M. / Noguchi, K. / Yamada, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3apt.cif.gz | 136.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3apt.ent.gz | 104.6 KB | Display | PDB format |
PDBx/mmJSON format | 3apt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/3apt ftp://data.pdbj.org/pub/pdb/validation_reports/ap/3apt | HTTPS FTP |
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-Related structure data
Related structure data | 3apyC 1v93S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 34648.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0327 / Plasmid: pET23, pET(tMRwt) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q5SLG6, methylenetetrahydrofolate reductase [NAD(P)H] #2: Chemical | ChemComp-FAD / | #3: Chemical | ChemComp-ACT / | #4: 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: 2.28 Å3/Da / Density % sol: 46.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.3 Details: PH 4.3-4.5, 293K, 0.2M SODIUM ACETATE, 1M LITHIUM CHROLIDE, 10% PEG 6000, 10-20% GLYCEROL, 2-5% DIOXANE, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 6, 2010 |
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→19.97 Å / Num. obs: 55102 / % possible obs: 99.54 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 4.83 / Num. unique all: 2689 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1V93 Resolution: 1.85→19.95 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.25234 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.21 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.06 Å2 / Biso mean: 35.903 Å2 / Biso min: 11.35 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.849→1.897 Å / Total num. of bins used: 20
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