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

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Basic information

Entry
Database: PDB / ID: 1fdt
TitleHUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 COMPLEXED WITH ESTRADIOL AND NADP+
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 dehydrogenase (NAD+) activity / testosterone biosynthetic process ...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 dehydrogenase (NAD+) activity / testosterone biosynthetic process / 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 / adipose tissue development / catalytic activity / skeletal muscle tissue development / steroid binding / bone development / gene expression / NADP binding / 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
ESTRADIOL / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 17-beta-hydroxysteroid dehydrogenase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 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-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, 1996-
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

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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)36,0864
Polymers34,9741
Non-polymers1,1123
Water2,468137
1
A: 17-BETA-HYDROXYSTEROID-DEHYDROGENASE
hetero molecules

A: 17-BETA-HYDROXYSTEROID-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1728
Polymers69,9482
Non-polymers2,2246
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9360 Å2
ΔGint-83 kcal/mol
Surface area20980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.770, 43.790, 60.530
Angle α, β, γ (deg.)90.00, 99.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-391-

HOH

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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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EST / ESTRADIOL / Estradiol


Mass: 272.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24O2 / Comment: hormone*YM
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 48 % / Description: R MERGE BETWEEN THE TWO DATA SETS: 0.078
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: 130 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Feb 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 13157 / % possible obs: 73.6 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rsym value: 0.058 / Net I/σ(I): 14.8
Reflection shellResolution: 2.15→2.34 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.39
Reflection
*PLUS
Num. measured all: 29073 / Rmerge(I) obs: 0.058

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENV. 2.0data reduction
XENGENV. 2.0data scaling
X-PLOR3.1phasing
RefinementResolution: 2.2→10 Å / σ(F): 2
Details: THE OCCUPANCY OF RESIDUE 360 (NADP+) HAS BEEN SET TO 0.5, ACCORDING TO ELECTRON DENSITY AND B-FACTOR. THE RIBOSE PUCKER (C2'-ENDO) HAS BEEN CONSTRAINED THROUGH DIHEDRAL CONSTRAINT SPECIFIED IN THE INPUT FILE.
RfactorNum. reflection% reflection
Rfree0.243 -10 %
Rwork0.193 --
obs0.193 13396 84.8 %
Displacement parametersBiso mean: 19.3 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 73 137 2391
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.02
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: 2.2→2.24 Å
RfactorNum. reflection% reflection
Rwork0.221 418 -
obs--53 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Type: x_improper_angle_deg / Dev ideal: 1.63

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