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Yorodumi- PDB-2g89: L. casei thymidylate synthase Y261A in complex with substrate, dUMP -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g89 | ||||||
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Title | L. casei thymidylate synthase Y261A in complex with substrate, dUMP | ||||||
Components | thymidylate synthase | ||||||
Keywords | TRANSFERASE / alpha/beta protein / beta sheet / dUMP-binding residue / dUMP complex / active site mutation | ||||||
Function / homology | Function and homology information thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytoplasm Similarity search - Function | ||||||
Biological species | Lactobacillus casei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å | ||||||
Authors | Finer-Moore, J.S. / Stroud, R.M. | ||||||
Citation | 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 | 2g89.cif.gz | 79.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g89.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 2g89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/2g89 ftp://data.pdbj.org/pub/pdb/validation_reports/g8/2g89 | HTTPS FTP |
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-Related structure data
Related structure data | 2g86C 2g8aC 2g8dC 2g8o 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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Details | The biological assembly is a dimer, generated by applying the transformation y-x,y,-1/2-z to the fractional coordinates in the assymetric unit, or by transforming the orthogonal coordinates (in angstroms) according to -x,y,-121.0-z |
-Components
#1: Protein | Mass: 36538.359 Da / Num. of mol.: 1 / Mutation: Y261A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus casei (bacteria) / Gene: THYA / Plasmid: pSCTS9 / Production host: Escherichia coli (E. coli) / Strain (production host): chi2913recA / References: UniProt: P00469, thymidylate synthase |
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#2: Chemical | ChemComp-UMP / |
#3: 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: 2.94 Å3/Da / Density % sol: 58.16 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: protein in 20mM KPO4 buffer with 15-20mM ammonium sulfate, DTT and 38mM dUMP, against 20mM KPO4 buffer alone, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1996 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→39.34 Å / Num. obs: 14146 / % possible obs: 78 % / Observed criterion σ(I): -3 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.4→2.55 Å / % possible all: 64.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.5→39.34 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2448052.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: RESTRAINED REFINEMENT WITH CNS, FINAL ROUND OF RESTRAINED REFINEMENT WITH REFMAC5
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.94 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→39.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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