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Yorodumi- PDB-2vf0: CRYSTAL STRUCTURE OF THE THYMIDYLATE SYNTHASE K48Q COMPLEXED WITH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vf0 | ||||||
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Title | CRYSTAL STRUCTURE OF THE THYMIDYLATE SYNTHASE K48Q COMPLEXED WITH 5NO2DUMP AND BW1843U89 | ||||||
Components | THYMIDYLATE SYNTHASE | ||||||
Keywords | TRANSFERASE / NUCLEOTIDE BIOSYNTHESIS / SUBSTRATE ANOLOGUE / ANTIFOLATE BINDING / RNA-BINDING / METHYLTRANSFERASE / REPRESSOR / BW1843U89 / CYTOPLASM / 5-NO2-DUMP / THYMIDYLATE SYNTHASE / TRANSLATION REGULATION | ||||||
Function / homology | Function and homology information thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / response to radiation / regulation of translation / methylation / magnesium ion binding / protein homodimerization activity / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Sotelo-Mundo, R.R. / Arreola, R. / Maley, F. / Montfort, W.R. | ||||||
Citation | Journal: Int.J.Biochem.Cell Biol. / Year: 2008 Title: Role of an Invariant Lysine Residue in Folate Binding on Escherichia Coli Thymidylate Synthase: Calorimetric and Crystallographic Analysis of the K48Q Mutant. Authors: Arvizu-Flores, A.A. / Sugich-Miranda, R. / Arreola, R. / Garcia-Orozco, K.D. / Velazquez-Contreras, E.F. / Montfort, W.R. / Maley, F. / Sotelo-Mundo, R.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vf0.cif.gz | 121.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vf0.ent.gz | 95.9 KB | Display | PDB format |
PDBx/mmJSON format | 2vf0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/2vf0 ftp://data.pdbj.org/pub/pdb/validation_reports/vf/2vf0 | HTTPS FTP |
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-Related structure data
Related structure data | 2vetC 3b5bC 1fflS 1fwmS 2g8o 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
#1: Protein | Mass: 30558.615 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: MUTANT K48Q COMPLEXED WITH 5-NO2DUMP AND BW1843U89 / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21 / Plasmid: PET17B / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A884, thymidylate synthase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Nonpolymer details | 5-DIHYDROXYAMINO,2'-DEOXYURIDINE 5'-MONOPHOSPHATE (NDU): COVALENT LINK BETWEEN CYS 146 AND NDU 1265 ...5-DIHYDROXYA | |
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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: 2.6 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 20 MM POTASSIUM PHOSPHATE BUFFER, 4 MM DTT AND INCREMENTS IN AMMONIUM SULFATE FROM 2.05 TO 2.6 M, PH 7.5 TO 8 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS / Detector: AREA DETECTOR / Date: Nov 22, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→35.58 Å / Num. obs: 15793 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 3.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1FFL AND 1FWM Resolution: 3→33.98 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2316773.83 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.1663 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→33.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
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Xplor file |
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