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Yorodumi- PDB-1e3w: Rat brain 3-hydroxyacyl-CoA dehydrogenase binary complex with NAD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e3w | ||||||
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Title | Rat brain 3-hydroxyacyl-CoA dehydrogenase binary complex with NADH and 3-keto butyrate | ||||||
Components | (SHORT CHAIN 3-HYDROXYACYL-COA ...) x 2 | ||||||
Keywords | DEHYDROGENASE / BETA-OXIDATION OF FATTY ACIDS / STEROIDS / AMYLOID BINDING | ||||||
Function / homology | Function and homology information brexanolone metabolic process / isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity / Mitochondrial protein degradation / mitochondrial tRNA methylation / chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity / mitochondrial tRNA 3'-end processing / acetoacetyl-CoA reductase activity ...brexanolone metabolic process / isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity / Mitochondrial protein degradation / mitochondrial tRNA methylation / chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity / mitochondrial tRNA 3'-end processing / acetoacetyl-CoA reductase activity / Branched-chain amino acid catabolism / 7alpha-hydroxysteroid dehydrogenase / mitochondrial ribonuclease P complex / mitochondrial tRNA 5'-end processing / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / cholate 7-alpha-dehydrogenase activity / C21-steroid hormone metabolic process / testosterone dehydrogenase [NAD(P)+] activity / tRNA methyltransferase complex / 3-hydroxyacyl-CoA dehydrogenase / isoleucine catabolic process / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / 3-hydroxyacyl-CoA dehydrogenase activity / testosterone dehydrogenase (NAD+) activity / Leydig cell differentiation / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / bile acid biosynthetic process / steroid catabolic process / estrogen metabolic process / fatty acid beta-oxidation / mitochondrial nucleoid / androgen metabolic process / steroid binding / mitochondrion organization / fatty acid metabolic process / nuclear estrogen receptor binding / male gonad development / NAD binding / amyloid-beta binding / protein homotetramerization / tRNA binding / endoplasmic reticulum / mitochondrion / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Powell, A.J. / Read, J.A. / Brady, R.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Recognition of Structurally Diverse Substrates by Type II 3-Hydroxyacyl-Coa Dehydrogenase (Hadh II) Amyloid-Beta Binding Alcohol Dehydrogenase (Abad) Authors: Powell, A.J. / Read, J.A. / Banfield, M.J. / Gunn-Moore, F. / Yan, S.D. / Lustbader, J. / Stern, A.R. / Stern, D.M. / Brady, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e3w.cif.gz | 420.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e3w.ent.gz | 343.6 KB | Display | PDB format |
PDBx/mmJSON format | 1e3w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e3w_validation.pdf.gz | 714.5 KB | Display | wwPDB validaton report |
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Full document | 1e3w_full_validation.pdf.gz | 755.5 KB | Display | |
Data in XML | 1e3w_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 1e3w_validation.cif.gz | 45 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/1e3w ftp://data.pdbj.org/pub/pdb/validation_reports/e3/1e3w | HTTPS FTP |
-Related structure data
Related structure data | 1e3sC 1e6wC 2hsdS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-SHORT CHAIN 3-HYDROXYACYL-COA ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 27244.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Cellular location: CYTOPLASM / Organ: BRAIN / Organelle: MITOCHONRIA / Plasmid: PET15B / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: O70351, 3-hydroxyacyl-CoA dehydrogenase |
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#2: Protein | Mass: 27272.510 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Cellular location: CYTOPLASM / Organ: BRAIN / Organelle: MITOCHONRIA / Plasmid: PET15B / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: O70351, 3-hydroxyacyl-CoA dehydrogenase |
-Non-polymers , 5 types, 902 molecules
#3: Chemical | ChemComp-NAD / #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-AAE / | #7: 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: 2.25 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: HANGING DROP PROT: 10MG/ML, 0.4 MM ACETOACETYL COA, 1 MM NADH, 10 MM HEP WELL: 28% PEG 4000, 0.2 M LI SO4, 0.1 M TRIS PH 8.5. 18 C | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.5 / 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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9091 |
Detector | Type: MARRESEARCH / Detector: CCD / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9091 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→40 Å / Num. obs: 148442 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.4→1.42 Å / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.291 / % possible all: 60.4 |
Reflection | *PLUS % possible obs: 92 % / Rmerge(I) obs: 0.06 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HSD Resolution: 2→40 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 18.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→40 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 141062 / Num. reflection Rfree: 7380 / Rfactor obs: 0.157 / Rfactor Rfree: 0.196 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 17.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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