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Yorodumi- PDB-1bq1: E. COLI THYMIDYLATE SYNTHASE MUTANT N177A IN COMPLEX WITH CB3717 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bq1 | ||||||
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Title | E. COLI THYMIDYLATE SYNTHASE MUTANT N177A IN COMPLEX WITH CB3717 AND 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP) | ||||||
Components | THYMIDYLATE SYNTHASE | ||||||
Keywords | TRANSFERASE / ACTIVE SITE MUTANT / REACTION INTERMEDIATE | ||||||
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: 2.5 Å | ||||||
Authors | Reyes, C.L. / Sage, C.R. / Rutenber, E.E. / Finer-Moore, J.S. / Stroud, R.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Inactivity of N229A thymidylate synthase due to water-mediated effects: isolating a late stage in methyl transfer. Authors: Reyes, C.L. / Sage, C.R. / Rutenber, E.E. / Nissen, R.M. / 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 | 1bq1.cif.gz | 146.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bq1.ent.gz | 123.7 KB | Display | PDB format |
PDBx/mmJSON format | 1bq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/1bq1 ftp://data.pdbj.org/pub/pdb/validation_reports/bq/1bq1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.999813, -0.01879, 0.004533), Vector: |
-Components
#1: Protein | Mass: 30516.643 Da / Num. of mol.: 2 / Mutation: N177A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: X2913 / Gene: THYA / Plasmid: PTHYA-N177A / Gene (production host): 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 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 52.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU R-AXIS II / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 9, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 23346 / % possible obs: 87.7 % / Observed criterion σ(I): 1 / Redundancy: 7.6 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.4 |
Reflection shell | Highest resolution: 2.4 Å / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2.5 / % possible all: 73.8 |
Reflection | *PLUS Num. measured all: 160471 |
Reflection shell | *PLUS % possible obs: 73.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→7 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 21.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.65 Å / Rfactor Rfree error: 0.017
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.333 / Rfactor obs: 0.241 |