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Yorodumi- PDB-1dhj: LONG-RANGE STRUCTURAL EFFECTS IN A SECOND-SITE REVERTANT OF A MUT... -
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-Basic information
Entry | Database: PDB / ID: 1dhj | ||||||
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Title | LONG-RANGE STRUCTURAL EFFECTS IN A SECOND-SITE REVERTANT OF A MUTANT DIHYDROFOLATE REDUCTASE | ||||||
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: 1.8 Å | ||||||
Authors | Brown, K.A. / Kraut, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 Title: Long-range structural effects in a second-site revertant of a mutant dihydrofolate reductase. Authors: Brown, K.A. / Howell, E.E. / Kraut, J. #1: Journal: Biochemistry / Year: 1993 Title: How Do Mutation at Phenylalanine-153 and Isoleucine-155 Partially Suppress the Effects of the Aspartate-27-> Serine Mutation in Escherichia Coli Dihydrofolate Reductase Authors: Dion, A. / Linn, C.E. / Bradrick, T.D. / Georghiou, S. / Howell, E.E. #2: Journal: J.Biol.Chem. / Year: 1990 Title: Role of Aspartate 27 of Dihydrofolate Reductase from Escherichia Coli in Interconversion of Active and Inactive Enzyme Conformers and the Binding of Nadph Authors: Appleman, J.R. / Howell, E.E. / Kraut, J. / Blakely, R.L. #3: Journal: Biochemistry / Year: 1990 Title: A Second-Site Mutation at Phenylalanine-137 that Increases Catalytic Efficiency in the Mutant Aspartate-27-> Serine Escherichia Coli Dihydrofolate Reductase Authors: Howell, E.E. / Booth, C. / Farnum, M. / Kraut, J. / Warren, M.S. #4: Journal: Biochemistry / Year: 1990 Title: Dihydrofolate Reductase from Escherichia Coli: Probing the Role of Aspartate-27 and Phenylalanine-137 in Enzyme Conformation and the Binding of Nadph Authors: Dunn, S.M. / Lanigan, T.M. / Howell, E.E. #5: Journal: Science / Year: 1986 Title: Functional Role of Aspartic Acid-27 in Dihydrofolate Reductase Revealed by Mutagenesis Authors: Howell, E.E. / Villafranca, J.E. / Waren, M.S. / Oatley, S.J. / Kraut, J. #6: Journal: Biochemistry / Year: 1982 Title: Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase 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. #7: 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 | 1dhj.cif.gz | 88.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dhj.ent.gz | 66.9 KB | Display | PDB format |
PDBx/mmJSON format | 1dhj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/1dhj ftp://data.pdbj.org/pub/pdb/validation_reports/dh/1dhj | 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 = 3.10 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: GLY B 95 - GLY B 96 OMEGA = 0.54 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.92724, -0.36739, 0.07245), 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: 17932.221 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 | SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.51 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.8 / Method: unknown / Details: referred to J.Biol.Chem. 257.13650-13662 1982 | ||||||||||||||||||||
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: 1.8 Å / Num. obs: 32933 / % possible obs: 99 % / Rmerge(I) obs: 0.039 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.167 / Highest resolution: 1.8 Å | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.8 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Num. reflection all: 32933 / Rfactor obs: 0.167 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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