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- PDB-1ddu: E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH CB3717 AND 2',5'-DID... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ddu | ||||||
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Title | E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH CB3717 AND 2',5'-DIDEOXYURIDINE (DDURD) | ||||||
![]() | THYMIDYLATE SYNTHASE | ||||||
![]() | METHYLTRANSFERASE / TRANSFERASE (METHYLTRANSFERASE) / SUBSTRATE MODULES | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Stout, T.J. / Sage, C.R. / Stroud, R.M. | ||||||
![]() | ![]() Title: The additivity of substrate fragments in enzyme-ligand binding. Authors: Stout, T.J. / Sage, C.R. / Stroud, R.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.1 KB | Display | ![]() |
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PDB format | ![]() | 94.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 551 KB | Display | ![]() |
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Full document | ![]() | 572.7 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 21.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1an5C ![]() 1aobC ![]() 1bduC ![]() 1bidC ![]() 1tduSC ![]() 1tjsC ![]() 1trgC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-1, 0.01, -0.009), Vector: |
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Components
#1: Protein | Mass: 30543.662 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.4 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.8 Details: CRYSTALLIZATION WAS CONDUCTED IN HANGING DROPS CONTAINING 4.2 MG/ML E. COLI TS, 0.38 MM DURD, 3.8 MM DTT, 1.0 MM CB3717 AND 1.2 M (NH4)2SO4, PH 7.8 (20 MM KPO4) OVER A WELL SOLUTION ...Details: CRYSTALLIZATION WAS CONDUCTED IN HANGING DROPS CONTAINING 4.2 MG/ML E. COLI TS, 0.38 MM DURD, 3.8 MM DTT, 1.0 MM CB3717 AND 1.2 M (NH4)2SO4, PH 7.8 (20 MM KPO4) OVER A WELL SOLUTION CONTAINING 2.4 M (NH4)2SO4 AND 1.0 MM DTT., vapor diffusion - hanging drop | |||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 37027 / % possible obs: 70.1 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.252 / % possible all: 49.8 |
Reflection | *PLUS Num. obs: 25970 / Num. measured all: 55680 / Rmerge(I) obs: 0.133 |
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Processing
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 1TDU Resolution: 2.1→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 24.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.3 |