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- PDB-1qyx: Crystal structure of human estrogenic 17beta-hydroxysteroid dehyd... -

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Basic information

Entry
Database: PDB / ID: 1qyx
TitleCrystal structure of human estrogenic 17beta-hydroxysteroid dehydrogenase complex with androstenedione and NADP
ComponentsEstradiol 17 beta-dehydrogenase 1
KeywordsOXIDOREDUCTASE / 17bHSD1 / androstenedione / C19-steroid / NADP binding
Function / homology
Function and homology information


17-beta-hydroxysteroid dehydrogenase (NADP+) activity / 3(or 17)beta-hydroxysteroid dehydrogenase / estradiol binding / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)+] activity / cellular response to metal ion / Estrogen biosynthesis / : / testosterone biosynthetic process / testosterone dehydrogenase (NAD+) activity ...17-beta-hydroxysteroid dehydrogenase (NADP+) activity / 3(or 17)beta-hydroxysteroid dehydrogenase / estradiol binding / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)+] activity / cellular response to metal ion / Estrogen biosynthesis / : / 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 / cytosol / cytoplasm
Similarity search - Function
17beta-dehydrogenase / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-ANDROSTENE-3-17-DIONE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 17-beta-hydroxysteroid dehydrogenase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.89 Å
AuthorsShi, R. / Lin, S.X.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Cofactor hydrogen bonding onto the protein main chain is conserved in the short chain dehydrogenase/reductase family and contributes to nicotinamide orientation.
Authors: Shi, R. / Lin, S.X.
History
DepositionSep 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN Several atoms belonging to Nicotinamide part of HETNAM 'NAP' could not be modeled and are ...HETEROGEN Several atoms belonging to Nicotinamide part of HETNAM 'NAP' could not be modeled and are missing from the coordinates

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Estradiol 17 beta-dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0104
Polymers34,8881
Non-polymers1,1223
Water2,072115
1
A: Estradiol 17 beta-dehydrogenase 1
hetero molecules

A: Estradiol 17 beta-dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0198
Polymers69,7762
Non-polymers2,2446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8620 Å2
ΔGint-33 kcal/mol
Surface area21750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.700, 44.030, 60.790
Angle α, β, γ (deg.)90.00, 99.52, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly (homodimer) is generated by the two fold axis: -X, Y, -Z.

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Components

#1: Protein Estradiol 17 beta-dehydrogenase 1 / 17-beta-HSD 1 / Placental 17-beta-hydroxysteroid dehydrogenase / 20 alpha- hydroxysteroid ...17-beta-HSD 1 / Placental 17-beta-hydroxysteroid dehydrogenase / 20 alpha- hydroxysteroid dehydrogenase / 20-alpha-HSD / E2DH


Mass: 34887.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: placenta
References: UniProt: P14061, 17beta-estradiol 17-dehydrogenase
#2: Chemical ChemComp-ASD / 4-ANDROSTENE-3-17-DIONE


Mass: 286.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26O2 / Comment: hormone*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, magnisum chloride, beta-octylglucoside, HEPES, glycerol, soaking with testosterone and NADP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.89→30 Å / Num. all: 65964 / Num. obs: 24387 / % possible obs: 95.4 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.046
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 2.58 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 2 / Num. unique all: 2478 / % possible all: 93.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1JTV

1jtv


Resolution: 1.89→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.227 1230 random
Rwork0.186 --
obs-24122 -
Displacement parametersBiso mean: 37.7 Å2
Refinement stepCycle: LAST / Resolution: 1.89→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2120 0 54 115 2289
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.012
X-RAY DIFFRACTIONr_angle_refined_deg1.7
LS refinement shellResolution: 1.89→1.97 Å
RfactorNum. reflection
Rfree0.329 139
Rwork0.24 -
obs-2731

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