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- PDB-1ooe: Structural Genomics of Caenorhabditis elegans : Dihydropteridine ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ooe | ||||||
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Title | Structural Genomics of Caenorhabditis elegans : Dihydropteridine reductase | ||||||
![]() | Dihydropteridine reductase | ||||||
![]() | OXIDOREDUCTASE / Structural Genomics / Dihydropteridine reductase / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG | ||||||
Function / homology | ![]() Phenylalanine metabolism / 6,7-dihydropteridine reductase activity / NADH binding / tetrahydrobiopterin biosynthetic process / L-phenylalanine catabolic process / NADPH binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Symersky, J. / Li, S. / Nagy, L. / Qiu, S. / Lin, G. / Tsao, J. / Luo, D. / Carson, M. / DeLucas, L. / Luo, M. / Southeast Collaboratory for Structural Genomics (SECSG) | ||||||
![]() | ![]() Title: Structural genomics of Caenorhabditis elegans: structure of dihydropteridine reductase. Authors: Symersky, J. / Li, S. / Carson, M. / Luo, D. / Luan, C.H. / Luo, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.6 KB | Display | ![]() |
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PDB format | ![]() | 85 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.4 KB | Display | ![]() |
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Full document | ![]() | 450.6 KB | Display | |
Data in XML | ![]() | 25.2 KB | Display | |
Data in CIF | ![]() | 38.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dhrS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24734.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.5 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K RESERVOIR: 20% PEG8000, 10 MM MGCL2, 0.1 M AMMONIUM SULFATE, 50 MM MES, PH 5.6; PROTEIN STOCK: 17.3 MG/ML IN 10 MM HEPES, PH 7.0; ...Details: pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K RESERVOIR: 20% PEG8000, 10 MM MGCL2, 0.1 M AMMONIUM SULFATE, 50 MM MES, PH 5.6; PROTEIN STOCK: 17.3 MG/ML IN 10 MM HEPES, PH 7.0; DROPS: 2 MICROLITERS OF PROTEIN STOCK + 4 MICROLITERS OF RESERVOIR SOLUTION | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 295 K / pH: 7 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 3, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07175 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 56662 / Num. obs: 56662 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.041 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 0.8 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 2969 / Rsym value: 0.281 / % possible all: 74 |
Reflection | *PLUS Highest resolution: 1.65 Å / Lowest resolution: 32.28 Å / % possible obs: 95.3 % / Num. measured all: 102854 / Rmerge(I) obs: 0.041 |
Reflection shell | *PLUS Highest resolution: 1.65 Å / Lowest resolution: 1.71 Å / % possible obs: 93.8 % / Rmerge(I) obs: 0.281 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1DHR Resolution: 1.65→32.28 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000 / Data cutoff high rms absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: THE ELECTRON DENSITY AND RSR VALUE SUPPORT THE CONFORMATION OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.9819 Å2 / ksol: 0.294278 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.1 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→32.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.71 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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