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Yorodumi- PDB-1gz6: (3R)-HYDROXYACYL-COA DEHYDROGENASE FRAGMENT OF RAT PEROXISOMAL MU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gz6 | ||||||
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Title | (3R)-HYDROXYACYL-COA DEHYDROGENASE FRAGMENT OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE 2 | ||||||
Components | ESTRADIOL 17 BETA-DEHYDROGENASE 4 | ||||||
Keywords | DEHYDROGENASE / 17BETA-HSD4 / MFE-2 / BETA-OXIDATION / PEROXISOME / SDR / STEROID BIOSYNTHESIS / OXIDOREDUCTASE / NADP / MULTIGENE FAMIL | ||||||
Function / homology | Function and homology information Beta-oxidation of pristanoyl-CoA / : / alpha-linolenic acid (ALA) metabolism / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / 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 / medium-chain fatty-acyl-CoA metabolic process / : / Beta-oxidation of very long chain fatty acids ...Beta-oxidation of pristanoyl-CoA / : / alpha-linolenic acid (ALA) metabolism / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / 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 / medium-chain fatty-acyl-CoA metabolic process / : / Beta-oxidation of very long chain fatty acids / enoyl-CoA hydratase 2 / 3-hydroxyacyl-CoA dehydratase activity / Peroxisomal protein import / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / testosterone dehydrogenase [NAD(P)] activity / very long-chain fatty acid metabolic process / : / response to xenobiotic stimulus => GO:0009410 / 3-hydroxyacyl-CoA dehydrogenase activity / Sertoli cell development / estradiol 17-beta-dehydrogenase [NAD(P)] activity / enoyl-CoA hydratase activity / response to steroid hormone / estrogen metabolic process / fatty acid beta-oxidation / androgen metabolic process / cellular response to organic cyclic compound / isomerase activity / cholesterol metabolic process / response to organic cyclic compound / peroxisome / protein homodimerization activity / identical protein binding Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.38 Å | ||||||
Authors | Haapalainen, A.M. / Hiltunen, J.K. / Glumoff, T. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Binary Structure of the Two-Domain (3R)-Hydroxyacyl-Coa Dehydrogenase from Rat Peroxisomal Multifunctional Enzyme Type 2 at 2.38 A Resolution Authors: Haapalainen, A.M. / Koski, M.K. / Qin, Y.M. / Hiltunen, J.K. / Glumoff, T. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gz6.cif.gz | 250.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gz6.ent.gz | 209.6 KB | Display | PDB format |
PDBx/mmJSON format | 1gz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/1gz6 ftp://data.pdbj.org/pub/pdb/validation_reports/gz/1gz6 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9884, -0.0005, 0.1522), Vector: |
-Components
#1: Protein | Mass: 34822.527 Da / Num. of mol.: 4 Fragment: (3R)-HYDROXYACYL-COA DEHYDROGENASE FRAGMENT, RESIDUES 1-319 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Organ: LIVER / Plasmid: PET3D/DHDELTASCP-2LDELTA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P97852, 17beta-estradiol 17-dehydrogenase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-NAI / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.5 Details: 21 % PEG 6000, 0.2 M LITHIUM SULFATE 0.1 M NA-CACODYLATE, PH 5.5, 10 MM NAD+, 0.23 MM TRITON X-100 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979578,0.979269,0.972433 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 2000 / Details: MIRRORS | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.38→20 Å / Num. obs: 55717 / % possible obs: 99.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 12.9 | ||||||||||||
Reflection shell | Resolution: 2.38→2.46 Å / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 6.6 / % possible all: 98.4 | ||||||||||||
Reflection | *PLUS Lowest resolution: 24 Å | ||||||||||||
Reflection shell | *PLUS % possible obs: 98.4 % / Num. unique obs: 5466 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.38→20 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 69.1235 Å2 / ksol: 0.352456 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.38→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.38→2.52 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: NAI_XPLOR_PAR.TXT / Topol file: NAI_XPLOR_TOP.TXT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Num. reflection all: 55603 / Num. reflection obs: 52794 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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