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- PDB-2p4t: Structure of the Q67H mutant of R67 dihydrofolate reductase-NADP+... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2p4t | ||||||
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Title | Structure of the Q67H mutant of R67 dihydrofolate reductase-NADP+ complex reveals a novel cofactor binding mode | ||||||
![]() | Dihydrofolate reductase type 2 | ||||||
![]() | OXIDOREDUCTASE / bacterial infections / folate metabolism / NADP+ / R67 DHFR / Symmetric binding / trimethoprim-resistance | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Divya, N. / Grifith, E. / Narayana, N. | ||||||
![]() | ![]() Title: Structure of the Q67H mutant of R67 dihydrofolate reductase-NADP+ complex reveals a novel cofactor binding mode. Authors: Divya, N. / Grifith, E. / Narayana, N. #1: ![]() Title: High-resolution structure of a plasmid-encoded dihydrofolate reductase: pentagonal network of water molecules in the D2-symmetric active site Authors: Narayana, N. #2: ![]() 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. / Xuong, N. #3: Journal: Protein Eng. / Year: 1997 Title: A glutamine 67-->histidine mutation in homotetrameric R67 dihydrofolate reductase results in four mutations per single active site pore and causes substantial substrate and cofactor inhibition Authors: Park, H. / Bradrick, T.D. / Howell, E.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 28.5 KB | Display | ![]() |
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PDB format | ![]() | 17.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 820.7 KB | Display | ![]() |
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Full document | ![]() | 825.6 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 8.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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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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: 6742.546 Da / Num. of mol.: 1 / Mutation: Residues 1-16 are cleaved and Q67H mutation 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: Chemical | ChemComp-NAP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Tris-Hcl buffer, 20% PEG1000 and 10% 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 210 / Detector: CCD / Date: Apr 23, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→20 Å / Num. all: 19048 / Num. obs: 18488 / % possible obs: 86.6 % / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Rsym value: 0.039 / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 1.15→1.24 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 1609 / Rsym value: 0.285 / % possible all: 60.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1VIE Resolution: 1.15→20 Å / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber Details: HOH 149 HAS PARTIAL OCCUPANCY. WHEN COFACTOR IS BOUND, THE HOH 149 IS ABSENT. HOH 146 ALSO HAS PARTIAL OCCUPANCY.THE ADENOSINE PHOSPHATE PORTION OF THE COFACTOR IS NOT SEEN IN THE DENSITY. ...Details: HOH 149 HAS PARTIAL OCCUPANCY. WHEN COFACTOR IS BOUND, THE HOH 149 IS ABSENT. HOH 146 ALSO HAS PARTIAL OCCUPANCY.THE ADENOSINE PHOSPHATE PORTION OF THE COFACTOR IS NOT SEEN IN THE DENSITY. THEREFORE, THE RESPECTIVE ATOMIC COORDINATES ARE MISSING IN THIS LIST.
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Refinement step | Cycle: LAST / Resolution: 1.15→20 Å
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LS refinement shell | Resolution: 1.15→1.24 Å
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