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Yorodumi- PDB-4gev: E. coli thymidylate synthase Y209W variant in complex with substr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gev | |||||||||
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Title | E. coli thymidylate synthase Y209W variant in complex with substrate and a cofactor analog | |||||||||
Components | Thymidylate synthase | |||||||||
Keywords | TRANSFERASE / beta sheet / alpha/beta protein / methylase | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å | |||||||||
Authors | Newby, Z. / Lee, T.T. / Finer-Moore, J. / Stroud, R.M. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2012 Title: A remote mutation affects the hydride transfer by disrupting concerted protein motions in thymidylate synthase. Authors: Wang, Z. / Abeysinghe, T. / Finer-Moore, J.S. / Stroud, R.M. / Kohen, A. #1: Journal: Biochemistry / Year: 2006 Title: The role of protein dynamics in thymidylate synthase catalysis: variants of conserved 2'-deoxyuridine 5'-monophosphate (dUMP)-binding Tyr-261. Authors: Newby, Z. / Lee, T.T. / Morse, R.J. / Liu, Y. / Liu, L. / Venkatraman, P. / Santi, D.V. / Finer-Moore, J.S. / Stroud, R.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gev.cif.gz | 345.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gev.ent.gz | 299.2 KB | Display | PDB format |
PDBx/mmJSON format | 4gev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gev_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4gev_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4gev_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 4gev_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/4gev ftp://data.pdbj.org/pub/pdb/validation_reports/ge/4gev | HTTPS FTP |
-Related structure data
Related structure data | 2g8o |
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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: 30582.697 Da / Num. of mol.: 2 / Mutation: Y209W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2827, JW2795, thyA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A884, thymidylate synthase #2: Chemical | #3: Chemical | #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: 2.5 Å3/Da / Density % sol: 50.78 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: vapor diffusion against 1.44 M Sodium citrate, HEPES from 5.2 mg/ml protein solution containing 17mM kPO4, DTT, 3.3 mM dUMP, 3.3 mM CB3717 and either 0.5% ethylacetate or 4% N-propanol, pH 7. ...Details: vapor diffusion against 1.44 M Sodium citrate, HEPES from 5.2 mg/ml protein solution containing 17mM kPO4, DTT, 3.3 mM dUMP, 3.3 mM CB3717 and either 0.5% ethylacetate or 4% N-propanol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 2, 2002 / Details: monochromator, double crystal Si (111) |
Radiation | Monochromator: double crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→45.834 Å / Num. all: 147002 / Num. obs: 146991 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 25.1 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.823 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→45.834 Å / Occupancy max: 1 / Occupancy min: 0.27 / SU ML: 0.3 / σ(F): 1.34 / Phase error: 13.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.878 Å2 / ksol: 0.388 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.3→45.834 Å
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Refine LS restraints |
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LS refinement shell |
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