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- PDB-1fds: HUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 COMPLEXED WITH ... -

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Basic information

Entry
Database: PDB / ID: 1fds
TitleHUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 COMPLEXED WITH 17-BETA-ESTRADIOL
Components17-BETA-HYDROXYSTEROID-DEHYDROGENASE
KeywordsDEHYDROGENASE / 17-BETA-HYDROXYSTEROID
Function / homology
Function and homology information


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
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
ESTRADIOL / 17-beta-hydroxysteroid dehydrogenase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR, molecular replacement / Resolution: 1.7 Å
AuthorsHousset, D. / Breton, R. / Mazza, C. / Fontecilla-Camps, J.-C.
Citation
Journal: Structure / Year: 1996
Title: The structure of a complex of human 17beta-hydroxysteroid dehydrogenase with estradiol and NADP+ identifies two principal targets for the design of inhibitors.
Authors: Breton, R. / Housset, D. / Mazza, C. / Fontecilla-Camps, J.C.
#1: 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.
History
DepositionJun 28, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: 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 ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / software / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 17-BETA-HYDROXYSTEROID-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2462
Polymers34,9741
Non-polymers2721
Water2,288127
1
A: 17-BETA-HYDROXYSTEROID-DEHYDROGENASE
hetero molecules

A: 17-BETA-HYDROXYSTEROID-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4934
Polymers69,9482
Non-polymers5452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6630 Å2
ΔGint-38 kcal/mol
Surface area22620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.330, 44.840, 60.960
Angle α, β, γ (deg.)90.00, 98.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 17-BETA-HYDROXYSTEROID-DEHYDROGENASE


Mass: 34973.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: unidentified baculovirus
References: UniProt: P14061, 17beta-estradiol 17-dehydrogenase
#2: Chemical ChemComp-EST / ESTRADIOL


Mass: 272.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24O2 / Comment: hormone*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.36 Å3/Da / Density % sol: 48 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Zhu, D.-W., (1993) J. Mol. Biol., 234, 242.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlenzyme1drop
22 mMbeta-octylglucoside1drop
320 %glycerol1drop
4100 mMHEPES1reservoir
5100 mM1reservoirMgCl2
624-26 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Mar 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→17 Å / Num. obs: 35032 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 20.4 Å2 / Rsym value: 0.05 / Net I/σ(I): 8.5
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.403 / % possible all: 93.5
Reflection
*PLUS
Num. measured all: 137576 / Rmerge(I) obs: 0.05

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMV. 5.2data reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR, molecular replacement
Starting model: CALPHAS OF 3ALPHA,20BETA HYDROXYSTEROID DEHYDROGENASE

Resolution: 1.7→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.203 -10 %
Rwork0.178 --
obs0.178 31798 88.3 %
Displacement parametersBiso mean: 25.8 Å2
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2152 0 20 127 2299
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.72
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_it3
X-RAY DIFFRACTIONx_mcangle_it4
X-RAY DIFFRACTIONx_scbond_it4
X-RAY DIFFRACTIONx_scangle_it5
LS refinement shellResolution: 1.7→1.73 Å
RfactorNum. reflection% reflection
Rwork0.241 946 -
obs--53 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Type: x_improper_angle_deg / Dev ideal: 1.33

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