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- PDB-1ru0: Crystal structure of DCoH2, a paralog of DCoH, the Dimerization C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ru0 | ||||||
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Title | Crystal structure of DCoH2, a paralog of DCoH, the Dimerization Cofactor of HNF-1 | ||||||
![]() | DcoH-like protein DCoHm | ||||||
![]() | LYASE / alpha and beta structure | ||||||
Function / homology | ![]() 4a-hydroxytetrahydrobiopterin dehydratase / 4-alpha-hydroxytetrahydrobiopterin dehydratase activity / phenylalanine 4-monooxygenase activity / tetrahydrobiopterin biosynthetic process / positive regulation of DNA-templated transcription / mitochondrion / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rose, R.B. / Pullen, K.E. / Bayle, J.H. / Crabtree, G.R. / Alber, T. | ||||||
![]() | ![]() Title: Biochemical and structural basis for partially redundant enzymatic and transcriptional functions of DCoH and DCoH2 Authors: Rose, R.B. / Pullen, K.E. / Bayle, J.H. / Crabtree, G.R. / Alber, T. #1: ![]() Title: Structural basis of dimerization, coactivator recognition and MODY3 mutations in HNF-1alpha Authors: Rose, R.B. / Bayle, J.H. / Endrizzi, J.A. / Cronk, J.D. / Crabtree, G.R. / Alber, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55 KB | Display | ![]() |
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PDB format | ![]() | 39.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.3 KB | Display | ![]() |
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Full document | ![]() | 433.5 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dcoS 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 | A dimer is in the asymmetric unit, which interacts with HNF-1. DCoH2 is a tetramer in solution. The tetramer is generated by rotating the dimer around the crystallographic two-fold axis: -x, -x+y, -z+1/3. |
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Components
#1: Protein | Mass: 11899.393 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9CZL5, 4a-hydroxytetrahydrobiopterin dehydratase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.92 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: isopropanol, PEG 4000, Na Hepes, 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 4 / Detector: CCD / Date: May 1, 2000 |
Radiation | Monochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 30110 / Num. obs: 30110 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 18.5 Å2 / Rsym value: 0.066 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 4325 / Rsym value: 0.253 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1DCO Resolution: 1.6→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 89.3426 Å2 / ksol: 0.414439 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å
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Xplor file |
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