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Yorodumi- PDB-5ior: Flavin-dependent thymidylate synthase in complex with FAD and 2'-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ior | ||||||||||||
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Title | Flavin-dependent thymidylate synthase in complex with FAD and 2'-deoxyuridine-5'-monosulfate | ||||||||||||
Components | Thymidylate synthase ThyX | ||||||||||||
Keywords | TRANSFERASE / FAD-dependent / nucleotide biosynthesis / reductive methylation | ||||||||||||
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: 1.95 Å | ||||||||||||
Authors | Bernard, S.M. / Stull, F.W. / Smith, J.L. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Biochemistry / Year: 2016 Title: Deprotonations in the Reaction of Flavin-Dependent Thymidylate Synthase. Authors: Stull, F.W. / Bernard, S.M. / Sapra, A. / Smith, J.L. / Zuiderweg, E.R. / Palfey, B.A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ior.cif.gz | 112.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ior.ent.gz | 84.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ior.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ior_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5ior_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5ior_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 5ior_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/5ior ftp://data.pdbj.org/pub/pdb/validation_reports/io/5ior | HTTPS FTP |
-Related structure data
Related structure data | 5ioqC 5iosC 5iotC 4gt9S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27503.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (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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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-DUS / |
#4: Chemical | ChemComp-RBF / |
#5: 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: 3.28 Å3/Da / Density % sol: 62.46 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 6.6 Details: 7% PEG 4K, 100 mM NaCl, 100 mM Na/K phosphate, pH 6.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→80.92 Å / Num. obs: 27043 / % possible obs: 99.7 % / Redundancy: 14.6 % / Net I/σ(I): 20.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GT9 Resolution: 1.95→80.92 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.761 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.107 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.196 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→80.92 Å
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Refine LS restraints |
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