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- PDB-1equ: TYPE 1 17-BETA HYDROXYSTEROID DEHYDROGENASE EQUILIN COMPLEXED WIT... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1equ | ||||||
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Title | TYPE 1 17-BETA HYDROXYSTEROID DEHYDROGENASE EQUILIN COMPLEXED WITH NADP+ | ||||||
![]() | PROTEIN (ESTRADIOL 17 BETA-DEHYDROGENASE 1) | ||||||
![]() | OXIDOREDUCTASE / HYDROXYSTEROID DEHYDROGENASE / SHORT CHAIN DEHYDROGENASE / REDUCTASE | ||||||
Function / homology | ![]() estradiol binding / 3(or 17)beta-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)+] activity / cellular response to metal ion / Estrogen biosynthesis / dihydrotestosterone 17-beta-dehydrogenase activity / testosterone biosynthetic process / testosterone dehydrogenase (NAD+) activity ...estradiol binding / 3(or 17)beta-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)+] activity / cellular response to metal ion / Estrogen biosynthesis / dihydrotestosterone 17-beta-dehydrogenase activity / testosterone biosynthetic process / testosterone dehydrogenase (NAD+) activity / testosterone 17-beta-dehydrogenase (NADP+) activity / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / steroid biosynthetic process / estrogen metabolic process / NADP+ binding / lysosome organization / The canonical retinoid cycle in rods (twilight vision) / small molecule binding / catalytic activity / adipose tissue development / skeletal muscle tissue development / steroid binding / bone development / NADP binding / gene expression / protein homodimerization activity / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sawicki, M.W. / Erman, M. / Puranen, T. / Vihko, P. / Ghosh, D. | ||||||
![]() | ![]() Title: Structure of the ternary complex of human 17beta-hydroxysteroid dehydrogenase type 1 with 3-hydroxyestra-1,3,5,7-tetraen-17-one (equilin) and NADP+. Authors: Sawicki, M.W. / Erman, M. / Puranen, T. / Vihko, P. / Ghosh, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124 KB | Display | ![]() |
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PDB format | ![]() | 96.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 599.9 KB | Display | ![]() |
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Full document | ![]() | 642.7 KB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 27.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bhsS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper: (Code: given Matrix: (0.96803, 0.240107, -0.072577), Vector: |
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Components
#1: Protein | Mass: 34887.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P14061, 17beta-estradiol 17-dehydrogenase #2: Chemical | #3: Chemical | ChemComp-EQI / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.48 % | ||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: VAP. DIFF. FROM 28% PEG 4000 IN HEPES BUFFER, PH 7.5, CONTAINING 1 MM EQUILIN, pH 7.50 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 26, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→99 Å / Num. obs: 11408 / % possible obs: 93.1 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 3→3.23 Å / Mean I/σ(I) obs: 1.7 / % possible all: 92 |
Reflection | *PLUS Num. measured all: 28469 |
Reflection shell | *PLUS % possible obs: 92 % / Mean I/σ(I) obs: 1.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BHS Resolution: 3→12 Å / Rfactor Rfree error: 0.03 / Cross valid method: THROUGHOUT / σ(F): 1 Details: THE EXTENDED LOOP REGION OF THE B SUBUNIT (186-200) WAS MODELED AFTER THE APO STRUCTURE EXTENDED LOOP
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Refinement step | Cycle: LAST / Resolution: 3→12 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 3→3.23 Å / Rfactor Rfree: 0.373 / Rfactor Rwork: 0.223 / Total num. of bins used: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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