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Yorodumi- PDB-1dyh: ISOMORPHOUS CRYSTAL STRUCTURES OF ESCHERICHIA COLI DIHYDROFOLATE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dyh | ||||||
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Title | ISOMORPHOUS CRYSTAL STRUCTURES OF ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE COMPLEXED WITH FOLATE, 5-DEAZAFOLATE AND 5,10-DIDEAZATETRAHYDROFOLATE: MECHANISTIC IMPLICATIONS | ||||||
Components | DIHYDROFOLATE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information methotrexate binding / dihydrofolic acid binding / response to methotrexate / dihydrofolate metabolic process / NADP+ binding / folic acid binding / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / dihydrofolate metabolic process / NADP+ binding / folic acid binding / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / response to antibiotic / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Reyes, V.M. / Kraut, J. | ||||||
Citation | Journal: Biochemistry / Year: 1995 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: Journal: Biochemistry / Year: 1991 Title: Crystal Structure of Unliganded Escherichia Coli Dihydrofolate Reductase. Ligand Induced Conformational Changes and Cooperativity Binding Authors: Bystroff, C. / Kraut, J. #2: Journal: Biochemistry / Year: 1990 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: Journal: Biochemistry / Year: 1990 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: Journal: J.Biol.Chem. / Year: 1982 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: Journal: J.Biol.Chem. / Year: 1982 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dyh.cif.gz | 87.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dyh.ent.gz | 66.5 KB | Display | PDB format |
PDBx/mmJSON format | 1dyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/1dyh ftp://data.pdbj.org/pub/pdb/validation_reports/dy/1dyh | 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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Atom site foot note | 1: GLY A 95 - GLY A 96 OMEGA = 2.11 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: GLY B 95 - GLY B 96 OMEGA = 359.95 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
-Components
#1: Protein | Mass: 18020.326 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0ABQ4, dihydrofolate reductase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.16 % | |||||||||||||||||||||||||
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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: 21817 / % possible obs: 88 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.038 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.149 / 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 all: 21817 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |