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- PDB-1dyi: ISOMORPHOUS CRYSTAL STRUCTURES OF ESCHERICHIA COLI DIHYDROFOLATE ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dyi | ||||||
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Title | ISOMORPHOUS CRYSTAL STRUCTURES OF ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE COMPLEXED WITH FOLATE, 5-DEAZAFOLATE AND 5,10-DIDEAZATETRAHYDROFOLATE: MECHANISTIC IMPLICATIONS | ||||||
![]() | DIHYDROFOLATE REDUCTASE | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / response to antibiotic / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Reyes, V.M. / Kraut, J. | ||||||
![]() | ![]() Title: Isomorphous crystal structures of Escherichia coli dihydrofolate reductase complexed with folate, 5-deazafolate, and 5,10-dideazatetrahydrofolate: mechanistic implications. Authors: Reyes, V.M. / Sawaya, M.R. / Brown, K.A. / Kraut, J. #1: ![]() Title: Crystal Structure of Unliganded Escherichia Coli Dihydrofolate Reductase. Ligand Induced Conformational Changes and Cooperativity Binding Authors: Bystroff, C. / Kraut, J. #2: ![]() Title: Crystal Structures of Escherichia Coli Dihydrofolate Reductase and Folate.Nadp+ Ternary Complex. Substrate Binding and a Model for the Transition State Authors: Bystroff, C. / Oatley, S.J. / Kraut, J. #3: ![]() Title: Crystal Structures of Recombinant Human Dihydrofolate Reductase Complexed with Folate and 5-Deazafolate Authors: Davies II, J.F. / Delcamp, T.J. / Prendergast, N.J. / Freisheim, J.H. / Kraut, J. #4: ![]() Title: Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase Refined at 1.7 Angstroms Resolution I. General Features and Binding of Methotrexate Authors: Bolin, J.T. / Filman, D.J. / Matthews, D.A. / Hamlin, R.C. / Kraut, J. #5: ![]() Title: Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase at 1.7 Angstroms Resolution. II. Environment of Bound Nadph and Implications for Catalysis Authors: Filman, D.J. / Bolin, J.T. / Matthews, D.A. / Kraut, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.5 KB | Display | ![]() |
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PDB format | ![]() | 66.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 523.8 KB | Display | ![]() |
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Full document | ![]() | 546.2 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Atom site foot note | 1: GLY A 95 - GLY A 96 OMEGA = 359.66 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: GLY B 95 - GLY B 96 OMEGA = 0.59 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
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Components
#1: Protein | Mass: 18020.326 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CA / | #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: 51.93 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.9 Å / Num. obs: 20666 / % possible obs: 84.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.046 |
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Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.137 / Highest resolution: 1.9 Å | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.9 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 20666 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |