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Yorodumi- PDB-2drc: INVESTIGATION OF THE FUNCTIONAL ROLE OF TRYPTOPHAN-22 IN ESCHERIC... -
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-Basic information
Entry | Database: PDB / ID: 2drc | ||||||
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Title | INVESTIGATION OF THE FUNCTIONAL ROLE OF TRYPTOPHAN-22 IN ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE BY SITE-DIRECTED MUTAGENESIS | ||||||
Components | DIHYDROFOLATE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / folic acid metabolic process / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / folic acid metabolic process / 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 | Brown, K.A. / Kraut, J. | ||||||
Citation | Journal: Biochemistry / Year: 1991 Title: Investigation of the functional role of tryptophan-22 in Escherichia coli dihydrofolate reductase by site-directed mutagenesis. Authors: Warren, M.S. / Brown, K.A. / Farnum, M.F. / Howell, E.E. / Kraut, J. #1: Journal: Biochemistry / Year: 1991 Title: Crystal Structure of Unliganded Escherichia Coli Dihydrofolate Reductase. Ligand-Induced Conformational Changes and Cooperativity in Binding Authors: Bystroff, C. / Kraut, J. #2: Journal: Biochemistry / Year: 1990 Title: Crystal Structures of Escherichia Coli Dihydrofolate Reductase: The Nadp+ Holoenzyme and the 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. / Ashford, V.A. / Freisheim, J.H. / Kraut, J. #4: Journal: Science / Year: 1986 Title: Functional Role of Aspartic Acid-27 in Dihydrofolate Reductase Revealed by Mutagenesis Authors: Howell, E.E. / Villafranca, J.E. / Warren, M.S. / Oatley, S.J. / Kraut, J. #5: 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. #6: Journal: J.Biol.Chem. / Year: 1982 Title: Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase Refined 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 | 2drc.cif.gz | 77.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2drc.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 2drc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/2drc ftp://data.pdbj.org/pub/pdb/validation_reports/dr/2drc | 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 ANGLE = 3.358 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: GLY B 95 - GLY B 96 OMEGA ANGLE = 1.837 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.92058, -0.38188, 0.08184), Vector: Details | THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. | |
-Components
#1: Protein | Mass: 17981.289 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 / | Sequence details | RESIDUE 154 IS GLU IN THE RT500 STRAIN. IN THE MB1428 STRAIN (PROTEIN DATA BANK ENTRY 4DFR), THIS ...RESIDUE 154 IS GLU IN THE RT500 STRAIN. IN THE MB1428 STRAIN (PROTEIN DATA BANK ENTRY 4DFR), THIS RESIDUE IS A LYS. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.69 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 30609 / % possible obs: 96 % / Rmerge(I) obs: 0.049 |
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-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.161 / Highest resolution: 1.9 Å Details: THE MOLECULE DESIGNATED AS CHAIN B BELOW IS PREFERRED FOR STRUCTURAL COMPARISONS BECAUSE IT IS MORE COMPLETE AND LESS PERTURBED BY INTERMOLECULAR CONTACTS. | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.9 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Rfactor obs: 0.161 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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