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Open data
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Basic information
Entry | Database: PDB / ID: 5eaj | ||||||
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Title | Crystal structure of DHFR in 0% Isopropanol | ||||||
![]() | Dihydrofolate reductase | ||||||
![]() | OXIDOREDUCTASE / dynamics | ||||||
Function / homology | ![]() methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic 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 / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cuneo, M.J. / Agarwal, P.K. | ||||||
![]() | ![]() Title: Modulating Enzyme Activity by Altering Protein Dynamics with Solvent. Authors: Duff Jr., M.R. / Borreguero, J.M. / Cuneo, M.J. / Ramanathan, A. / He, J. / Kamath, G. / Chennubhotla, S.C. / Meilleur, F. / Howell, E.E. / Herwig, K.W. / Myles, D.A.A. / Agarwal, P.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.6 KB | Display | ![]() |
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PDB format | ![]() | 66.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ujxC ![]() 1rd7S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18020.326 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: folA, AA953_06220, ABE89_23390, ABE90_01590, ABE91_11465, ABE92_27580, ABE93_03540, ABE94_26505, ABE95_19105, AC789_1c00510, ACM16_01115, ACM17_00910, ACM18_00225, ACM19_01115, ACM20_00925, ...Gene: folA, AA953_06220, ABE89_23390, ABE90_01590, ABE91_11465, ABE92_27580, ABE93_03540, ABE94_26505, ABE95_19105, AC789_1c00510, ACM16_01115, ACM17_00910, ACM18_00225, ACM19_01115, ACM20_00925, ACM21_22820, BN1008_2275, ECONIH1_00280, ECs0051, EL75_3711, EL79_3822, EL80_3768, HW43_03985, IY32_08385, JD73_13725, NMECO18_25965, PD07_16380, PU06_14795, PU15_01135, PU21_08285, PU33_00085, PU38_11910, PU53_21230, PU69_06270, PU71_09850, PU73_17465, RR31_00265, SK64_04362, SK65_04102, SK81_04106, SY51_00265, TZ57_00270, UC21_17710, UC41_15235, UN86_27670, UN92_06125, WQ64_08430, WQ65_17175, WQ66_04025, WQ69_03315, WQ70_09735, WQ71_08985, WQ72_04470, WQ73_14425, WQ74_13220, WQ77_00770, WQ79_09130, WQ84_04435, WQ86_16125, WQ88_00770, WQ91_15025, WQ92_19155, WQ95_08145, WQ99_15285, WR00_12370, WR01_07485, WR03_05655, WR04_00040, WR05_03890, WR12_01840, WR13_10745, WR16_15930, WR17_04125, WR18_06540, WR19_18465, WR23_10335, WR24_10640, XB00_01295, XB01_19915 Production host: ![]() ![]() References: UniProt: C3TR70, UniProt: P0ABQ4*PLUS, dihydrofolate reductase #2: Chemical | #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M CaCl2, 20-35 % (w/v) PEG 6000, 0.1M NaHEPES pH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 1, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→40 Å / Num. all: 38279 / Num. obs: 38279 / % possible obs: 99.1 % / Redundancy: 8.4 % / Biso Wilson estimate: 22.79 Å2 / Rmerge(I) obs: 0.061 / Χ2: 1.357 / Net I/av σ(I): 38.455 / Net I/σ(I): 15.8 / Num. measured all: 320420 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1RD7 Resolution: 1.701→38.916 Å / FOM work R set: 0.8315 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.42 Å2 / ksol: 0.359 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.52 Å2 / Biso mean: 30.72 Å2 / Biso min: 9.81 Å2
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Refinement step | Cycle: final / Resolution: 1.701→38.916 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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