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Yorodumi- PDB-1rb2: DIHYDROFOLATE REDUCTASE COMPLEXED WITH FOLATE AND NICOTINAMIDE AD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rb2 | ||||||
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Title | DIHYDROFOLATE REDUCTASE COMPLEXED WITH FOLATE AND NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE (OXIDIZED FORM) | ||||||
Components | DIHYDROFOLATE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / NADP / TRIMETHOPRIM RESISTANCE / METHOTREXATE RESISTANCE / ONE-CARBON METABOLISM | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Sawaya, M.R. / Kraut, J. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence. Authors: Sawaya, M.R. / 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 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rb2.cif.gz | 77.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rb2.ent.gz | 61.6 KB | Display | PDB format |
PDBx/mmJSON format | 1rb2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rb/1rb2 ftp://data.pdbj.org/pub/pdb/validation_reports/rb/1rb2 | HTTPS FTP |
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-Related structure data
Related structure data | 1dreC 1ra1C 1ra2SC 1ra3C 1ra8C 1ra9C 1rb3C 1rc4C 1rd7C 1re7C 1rf7C 1rg7C 1rh3C 1rx1C 1rx2C 1rx3C 1rx4C 1rx5C 1rx6C 1rx7C 1rx8C 1rx9C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.94836, -0.02338, 0.31635), Vector: |
-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) / Strain: RT500 / Plasmid: PRWA-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABQ4, dihydrofolate reductase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.1 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: macro seeding | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Nov 28, 1992 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→100 Å / Num. obs: 20914 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.098 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.149 / % possible all: 75 |
Reflection | *PLUS Num. measured all: 72595 / Rmerge(I) obs: 0.098 |
Reflection shell | *PLUS % possible obs: 75 % / Rmerge(I) obs: 0.149 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RA2 Resolution: 2.1→20 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: MOEWS AND KRETSINGER / Bsol: 158.3 Å2 / ksol: 0.758 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5-D / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.006 / Weight: 0.02 |