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- PDB-2gqv: High-resolution structure of a plasmid-encoded dihydrofolate redu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2gqv | ||||||
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Title | High-resolution structure of a plasmid-encoded dihydrofolate reductase: pentagonal network of water molecules in the D2-symmetric active site | ||||||
![]() | Dihydrofolate reductase type 2 | ||||||
![]() | OXIDOREDUCTASE / anisotropic refinement / atomic-resolution structure / folate metabolism / plasmid-encoded R67 DHFR / TMP-resistant DHFR | ||||||
Function / homology | ![]() response to methotrexate / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / response to xenobiotic stimulus / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Narayana, N. | ||||||
![]() | ![]() Title: High-resolution structure of a plasmid-encoded dihydrofolate reductase: pentagonal network of water molecules in the D(2)-symmetric active site. Authors: Narayana, N. #1: ![]() Title: A plasmid-encoded dihydrofolate reductase from trimethoprim-resistant bacteria has a novel D2-symmetric active site. Authors: Narayana, N. / Matthews, D.A. / Howell, E.E. / Nguyen-huu, X. #2: Journal: Biochemistry / Year: 1986 Title: Crystal structure of a novel trimethoprim-resistant dihydrofolate reductase specified in Escherichia coli by R-plasmid R67. Authors: Matthews, D.A. / Smith, S.L. / Baccanari, D.P. / Burchall, J.J. / Oatley, S.J. / Kraut, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 53.6 KB | Display | ![]() |
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PDB format | ![]() | 39 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1vieS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is comprised of four subunits generated by symmetry axes. The crystallographic 222 symmetry generates the biologically active tetramer. x,y,z; -x+1,-y+1,z; y,x,-z+1; -y+1,-x+1,-z+1 |
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Components
#1: Protein | Mass: 6732.528 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: TMP-RESISTANT, CONTAINING R67 DHFR OVERPRODUCING PLASMID PLZ1 Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Tris-Hcl buffer, 25% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 1 / Detector: CCD / Date: Mar 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9495 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→50 Å / Num. all: 22453 / Num. obs: 19914 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 8.5 % / Biso Wilson estimate: 9.7 Å2 / Rsym value: 0.042 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.1→1.14 Å / Rsym value: 0.34 / % possible all: 58 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1VIE Resolution: 1.1→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→10 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.1 Å / Rfactor Rfree error: 0.012
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