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

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Basic information

Entry
Database: PDB / ID: 1qyv
TitleCrystal structure of human estrogenic 17beta-hydroxysteroid dehydrogenase complex with NADP
ComponentsEstradiol 17 beta-dehydrogenase 1
KeywordsOXIDOREDUCTASE / 17bHSD1-cofactor complex
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
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: 1.81 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

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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)35,7233
Polymers34,8881
Non-polymers8352
Water2,720151
1
A: Estradiol 17 beta-dehydrogenase 1
hetero molecules

A: Estradiol 17 beta-dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4476
Polymers69,7762
Non-polymers1,6714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8190 Å2
ΔGint-40 kcal/mol
Surface area21860 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.399, 43.916, 60.450
Angle α, β, γ (deg.)90.00, 99.36, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is genearated 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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


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


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


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, magnisum chloride, beta-octylglucoside, HEPES, glycerol, soaking with 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: Apr 15, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.81→40 Å / Num. obs: 28701 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 3.55 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.049
Reflection shellResolution: 1.81→1.87 Å / Redundancy: 2.82 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2 / Num. unique all: 2669 / % possible all: 92.2

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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: 1.81→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.235 1450 random
Rwork0.191 --
obs-28494 -
Displacement parametersBiso mean: 35.3 Å2
Refinement stepCycle: LAST / Resolution: 1.81→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2116 0 54 151 2321
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.012
X-RAY DIFFRACTIONr_angle_refined_deg1.5
LS refinement shellResolution: 1.81→1.887 Å
RfactorNum. reflection
Rfree0.326 143
Rwork0.26 -
obs-3050

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