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- PDB-1ikt: LIGANDED STEROL CARRIER PROTEIN TYPE 2 (SCP-2) LIKE DOMAIN OF HUM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ikt | ||||||
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Title | LIGANDED STEROL CARRIER PROTEIN TYPE 2 (SCP-2) LIKE DOMAIN OF HUMAN MULTIFUNCTIONAL ENZYME TYPE 2 (MFE-2) | ||||||
![]() | ESTRADIOL 17 BETA-DEHYDROGENASE 4 | ||||||
![]() | OXIDOREDUCTASE / alfa-beta fold / protein-Triton X-100 complex / hydrophobic tunnel / exposed peroxisomal targeting signal type 1 (PTS1) | ||||||
Function / homology | ![]() 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase / 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity / very long-chain fatty-acyl-CoA metabolic process / Beta-oxidation of pristanoyl-CoA / TYSND1 cleaves peroxisomal proteins / medium-chain fatty-acyl-CoA metabolic process / (3R)-hydroxyacyl-CoA dehydrogenase (NAD+) activity / : / enoyl-CoA hydratase 2 / 3-hydroxyacyl-CoA dehydratase activity ...3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase / 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity / very long-chain fatty-acyl-CoA metabolic process / Beta-oxidation of pristanoyl-CoA / TYSND1 cleaves peroxisomal proteins / medium-chain fatty-acyl-CoA metabolic process / (3R)-hydroxyacyl-CoA dehydrogenase (NAD+) activity / : / enoyl-CoA hydratase 2 / 3-hydroxyacyl-CoA dehydratase activity / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / alpha-linolenic acid (ALA) metabolism / Beta-oxidation of very long chain fatty acids / very long-chain fatty acid metabolic process / 3-hydroxyacyl-CoA dehydrogenase activity / Sertoli cell development / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / enoyl-CoA hydratase activity / peroxisomal membrane / estrogen metabolic process / fatty acid beta-oxidation / peroxisomal matrix / androgen metabolic process / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / isomerase activity / Peroxisomal protein import / osteoblast differentiation / peroxisome / protein homodimerization activity / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Haapalainen, A.M. / van Aalten, D.M.F. / Glumoff, T. | ||||||
![]() | ![]() Title: Crystal structure of the liganded SCP-2-like domain of human peroxisomal multifunctional enzyme type 2 at 1.75 A resolution. Authors: Haapalainen, A.M. / van Aalten, D.M. / Merilainen, G. / Jalonen, J.E. / Pirila, P. / Wierenga, R.K. / Hiltunen, J.K. / Glumoff, 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 | ![]() | 40.4 KB | Display | ![]() |
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PDB format | ![]() | 26.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 631.5 KB | Display | ![]() |
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Full document | ![]() | 632.8 KB | Display | |
Data in XML | ![]() | 8.7 KB | Display | |
Data in CIF | ![]() | 11.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1c44S 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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Unit cell |
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Components
#1: Protein | Mass: 13264.468 Da / Num. of mol.: 1 / Fragment: C-terminal domain, Residues 618-736 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P51659, 17beta-estradiol 17-dehydrogenase | ||||
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#2: Chemical | #3: Chemical | ChemComp-OXN / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: ammonium sulfate, sodium chloride, Triton X-100, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: CCD / Date: Sep 16, 2000 / Details: Premirror, Bent mirror monochromator |
Radiation | Monochromator: Double crystal focussing monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. all: 11659 / Num. obs: 11659 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.031 / Rsym value: 0.031 / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 1.75→1.81 Å / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1132 / Rsym value: 0.259 / % possible all: 97.1 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 97.1 % / Num. unique obs: 1132 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1C44 Resolution: 1.75→18 Å / Isotropic thermal model: isotropic / Cross valid method: R-free / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 30.3 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.82 Å / Total num. of bins used: 9
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 18 Å / σ(F): 0 / % reflection Rfree: 4.2 % / Rfactor obs: 0.192 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.3 Å2 | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.278 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.225 |