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Yorodumi- PDB-1jom: THE CRYSTAL STRUCTURE OF THE BINARY COMPLEX BETWEEN FOLINIC ACID ... -
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-Basic information
Entry | Database: PDB / ID: 1jom | ||||||
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Title | THE CRYSTAL STRUCTURE OF THE BINARY COMPLEX BETWEEN FOLINIC ACID (LEUCOVORIN) AND E. COLI DIHYDROFOLATE REDUCTASE | ||||||
Components | DIHYDROFOLATE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / METHOTREXATE RESISTANCE / ONE-CARBON METABOLISM OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Reyes, V.M. / Lee, H. / Kraut, J. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Crystal structures of Escherichia coli dihydrofolate reductase complexed with 5-formyltetrahydrofolate (folinic acid) in two space groups: evidence for enolization of pteridine O4. Authors: Lee, H. / Reyes, V.M. / Kraut, J. #1: 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. #2: 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. #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: 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. #5: Journal: J.Biol.Chem. / Year: 1982 Title: Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase Refined at 1.7 A Resolution. II. Environment of Bound Nadph and Implications for Catalysis Authors: Filman, D.J. / Bolin, J.T. / Matthews, D.A. / Kraut, J. #6: Journal: J.Biol.Chem. / Year: 1982 Title: Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase Refined at 1.7 A Resolution. I. General Features and Binding of Methotrexate Authors: Bolin, J.T. / Filman, D.J. / Matthews, D.A. / Hamlin, R.C. / Kraut, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jom.cif.gz | 54.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jom.ent.gz | 38.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jom.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jom_validation.pdf.gz | 513.5 KB | Display | wwPDB validaton report |
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Full document | 1jom_full_validation.pdf.gz | 526.6 KB | Display | |
Data in XML | 1jom_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 1jom_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/1jom ftp://data.pdbj.org/pub/pdb/validation_reports/jo/1jom | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18020.326 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: IN BINARY COMPLEX WITH FOLINIC ACID (LEUCOVORIN) / Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0ABQ4, dihydrofolate reductase |
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-Non-polymers , 5 types, 217 molecules
#2: Chemical | ChemComp-CL / | ||
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#3: Chemical | ChemComp-CA / | ||
#4: Chemical | ChemComp-FFO / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.24 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
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: 15022 / % possible obs: 99.7 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.068 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | 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 Rfactor obs: 0.142 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |