+Open data
-Basic information
Entry | Database: PDB / ID: 4gtb | ||||||
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Title | T. Maritima FDTS with FAD, dUMP, and Raltitrexed. | ||||||
Components | Thymidylate synthase thyX | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Flavin-dependent thymidylate synthase / TM0449 / Raltitrexed / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information thymidylate synthase (FAD) / thymidylate synthase (FAD) activity / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / NADPH binding / flavin adenine dinucleotide binding / methylation Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Mathews, I.I. / Lesley, S.A. / Kohen, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Folate binding site of flavin-dependent thymidylate synthase. Authors: Koehn, E.M. / Perissinotti, L.L. / Moghram, S. / Prabhakar, A. / Lesley, S.A. / Mathews, I.I. / Kohen, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gtb.cif.gz | 113.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gtb.ent.gz | 85.6 KB | Display | PDB format |
PDBx/mmJSON format | 4gtb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/4gtb ftp://data.pdbj.org/pub/pdb/validation_reports/gt/4gtb | HTTPS FTP |
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-Related structure data
Related structure data | 4gt9C 4gtaC 4gtcC 4gtdC 4gteC 4gtfC 4gtlC 1o26S 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: 27503.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: thyX, thy1, TM_0449 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYT0, thymidylate synthase (FAD) |
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-Non-polymers , 5 types, 130 molecules
#2: Chemical | ChemComp-FAD / |
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#3: Chemical | ChemComp-UMP / |
#4: Chemical | ChemComp-D16 / |
#5: Chemical | ChemComp-CL / |
#6: 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: 3.38 Å3/Da / Density % sol: 63.63 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.58 Details: 3-6% PEG 4K (w/v), 200mM NaCl, 100 mM Na/K phosphate (pH 6.58), VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9809 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 27, 2011 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9809 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. all: 41254 / Num. obs: 41254 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.831 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3042 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1O26 Resolution: 1.7→39.09 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.959 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.076 / ESU R Free: 0.073 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.649 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→39.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -38.936 Å / Origin y: -5.013 Å / Origin z: 20.052 Å
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Refinement TLS group |
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