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Yorodumi- PDB-1drb: CRYSTAL STRUCTURE OF UNLIGANDED ESCHERICHIA COLI DIHYDROFOLATE RE... -
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-Basic information
Entry | Database: PDB / ID: 1drb | ||||||
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Title | CRYSTAL STRUCTURE OF UNLIGANDED ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE. LIGAND-INDUCED CONFORMATIONAL CHANGES AND COOPERATIVITY IN BINDING | ||||||
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: 1.96 Å | ||||||
Authors | David, C. / Kraut, J. | ||||||
Citation | 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. #1: 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. #2: 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. #3: 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. #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 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 | 1drb.cif.gz | 89.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1drb.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 1drb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/1drb ftp://data.pdbj.org/pub/pdb/validation_reports/dr/1drb | 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 = 2.170 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: GLY B 95 - GLY B 96 OMEGA ANGLE = 2.458 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.92457, -0.3749, 0.068), Vector: Details | THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. | |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 18008.381 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 |
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-Non-polymers , 5 types, 433 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.01 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5.4 / 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 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.96→5 Å Details: DURING THE REFINEMENT THE CALCIUM ION (DESIGNATED CA) AND THE TWO CHLORIDE IONS (DESIGNATED CL) WERE MODELED AS OXYGEN ATOMS.
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Refinement step | Cycle: LAST / Resolution: 1.96→5 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.96 Å / Lowest resolution: 5 Å / Num. reflection obs: 25191 / Rfactor obs: 0.149 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |