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Yorodumi- PDB-2aaz: Cryptococcus neoformans thymidylate synthase complexed with subst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aaz | ||||||
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Title | Cryptococcus neoformans thymidylate synthase complexed with substrate and an antifolate | ||||||
Components | Thymidylate synthase | ||||||
Keywords | TRANSFERASE / Methyl transferase / Nucleotide biosynthesis | ||||||
Function / homology | Function and homology information thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Filobasidiella neoformans (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Finer-Moore, J.S. / Anderson, A.C. / O'Neil, R.H. / Costi, M.P. / Ferrari, S. / Krucinski, J. / Stroud, R.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: The structure of Cryptococcus neoformans thymidylate synthase suggests strategies for using target dynamics for species-specific inhibition. Authors: Finer-Moore, J.S. / Anderson, A.C. / O'Neil, R.H. / Costi, M.P. / Ferrari, S. / Krucinski, J. / Stroud, R.M. #1: Journal: J.Med.Chem. / Year: 1999 Title: Phthalein derivatives as a new tool for selectivity in thymidylate synthase inhibition Authors: Costi, P.M. / Rinaldi, M. / Tondi, D. / Pecorari, P. / Barlocco, D. / Ghelli, S. / Stroud, R.M. / Santi, D.V. / Stout, T.J. / Musiu, C. / Marangiu, E.M. / Pani, A. / Congiu, D. / Loi, G.A. / La Colla, P. #2: Journal: Biochemistry / Year: 1999 Title: Structure-based design of inhibitors specific for bacterial thymidylate synthase Authors: Stout, T.J. / Tondi, D. / Rinaldi, M. / Barlocco, D. / Pecorari, P. / Santi, D.V. / Kuntz, I.D. / Stroud, R.M. / Shoichet, B.K. / Costi, M.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2aaz.cif.gz | 3.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2aaz.ent.gz | 3.1 MB | Display | PDB format |
PDBx/mmJSON format | 2aaz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/2aaz ftp://data.pdbj.org/pub/pdb/validation_reports/aa/2aaz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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8 |
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Unit cell |
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Number of models | 4 | ||||||||
Components on special symmetry positions |
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Details | The biological assembly is a dimer. There are 8 dimers in the asymmetric unit and four of these dimers are 4-fold statistically disordered. Pairs of chains that constitute the four fully-occupied biological dimers are (A,B), (C,D), (E,F) and (G,H). Dimers that are in four 1/4-occupied packing arrangements in the cell are chains (I,J), (K,L), (M,N) and (O,P) |
-Components
#1: Protein | Mass: 35911.977 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Filobasidiella neoformans (fungus) / Gene: TMP1 / Plasmid: pET CNTS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P45351, UniProt: P0CS12*PLUS, thymidylate synthase #2: Chemical | ChemComp-UMP / #3: Chemical | ChemComp-CB3 / #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: 2.93 Å3/Da / Density % sol: 57.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 0.107 mM protein, dUMP,CB3, DTT, PEG4000/PEG6000, Tris, Na acetate/K acetate, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 19, 2000 / Details: monochrometer |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→99 Å / Num. all: 389001 / Num. obs: 389001 / % possible obs: 97 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 1.85 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.07→2.14 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 1.7 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→49.91 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 5580798.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Tight NCS restraints used throughout refinement. Structures of all monomers in the asymmetric unit restrained to be equivalent except for the following C. neoformans thymidylate synthase ...Details: Tight NCS restraints used throughout refinement. Structures of all monomers in the asymmetric unit restrained to be equivalent except for the following C. neoformans thymidylate synthase inserts: residues 13-16, 107-108 200-202. The following residues not present in the model: 1-12 for chains A-H and side chain of K107 in chains A and C, residues 1-15 and 200-202 in chains I-P.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.4499 Å2 / ksol: 0.20613 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.08→49.91 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.08→2.21 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
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Xplor file |
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