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- PDB-1bhs: HUMAN ESTROGENIC 17BETA-HYDROXYSTEROID DEHYDROGENASE -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1bhs
TitleHUMAN ESTROGENIC 17BETA-HYDROXYSTEROID DEHYDROGENASE
Components17BETA-HYDROXYSTEROID DEHYDROGENASE
KeywordsOXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE / STEROID DEHYDROGENASE / ESTROGEN / HUMAN TYPE I 17BETA-HSD / HUMAN PLACENTAL 17BETA-HSD
Function / homology
Function and homology information


17-beta-hydroxysteroid dehydrogenase (NADP+) activity / 3(or 17)beta-hydroxysteroid dehydrogenase / cellular response to metal ion / estrogen biosynthetic process / estradiol binding / Estrogen biosynthesis / testosterone dehydrogenase (NADP+) activity / testosterone biosynthetic process / : / testosterone dehydrogenase (NAD+) activity ...17-beta-hydroxysteroid dehydrogenase (NADP+) activity / 3(or 17)beta-hydroxysteroid dehydrogenase / cellular response to metal ion / estrogen biosynthetic process / estradiol binding / Estrogen biosynthesis / testosterone dehydrogenase (NADP+) activity / testosterone biosynthetic process / : / testosterone dehydrogenase (NAD+) activity / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / steroid biosynthetic process / NADP+ binding / estrogen metabolic process / lysosome organization / small molecule binding / The canonical retinoid cycle in rods (twilight vision) / 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
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
17-beta-hydroxysteroid dehydrogenase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsGhosh, D.
Citation
Journal: Structure / Year: 1995
Title: Structure of human estrogenic 17 beta-hydroxysteroid dehydrogenase at 2.20 A resolution.
Authors: Ghosh, D. / Pletnev, V.Z. / Zhu, D.W. / Wawrzak, Z. / Duax, W.L. / Pangborn, W. / Labrie, F. / Lin, S.X.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of the Complex of Human Placental 17 Beta-Hydroxysteroid Dehydrogenase with Nadp+
Authors: Zhu, D.W. / Lee, X. / Breton, R. / Ghosh, D. / Pangborn, W. / Daux, W.L. / Lin, S.X.
History
DepositionApr 19, 1995Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 17BETA-HYDROXYSTEROID DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)34,8881
Polymers34,8881
Non-polymers00
Water88349
1
A: 17BETA-HYDROXYSTEROID DEHYDROGENASE

A: 17BETA-HYDROXYSTEROID DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)69,7762
Polymers69,7762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5200 Å2
ΔGint-41 kcal/mol
Surface area22670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)123.560, 45.050, 61.330
Angle α, β, γ (deg.)90.00, 99.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 17BETA-HYDROXYSTEROID DEHYDROGENASE / TYPE I 17BETA-HYDROXYSTEROID DEHYDROGENASE


Mass: 34887.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P14061, 17beta-estradiol 17-dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 45 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
20.075 M1dropMgCl2
30.05 MHEPES1drop
414 %PEG40001drop
510 %glycerol1drop
60.15 M1reservoirMgCl2
70.1 MHEPES1reservoir
827 %PEG40001reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 16, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 14079 / % possible obs: 81 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.064
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. measured all: 43960
Reflection shell
*PLUS
Mean I/σ(I) obs: 2.5

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Processing

Software
NameClassification
X-PLORrefinement
RIGAKUdata reduction
RefinementResolution: 2.2→8 Å / σ(F): 1
Details: THE REGION 192 - 200 IS VERY POORLY DEFINED IN THE ELECTRON DENSITY MAPS AND WAS MODELED STEREOCHEMICALLY.
RfactorNum. reflection
Rfree0.229 -
Rwork0.185 -
obs0.185 13474
Displacement parametersBiso mean: 39 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2177 0 0 49 2226
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.68
X-RAY DIFFRACTIONx_dihedral_angle_deg23.55

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