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- PDB-7x3z: Crystal structure of human 17beta-hydroxysteroid dehydrogenase ty... -

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Basic information

Entry
Database: PDB / ID: 7x3z
TitleCrystal structure of human 17beta-hydroxysteroid dehydrogenase type 1 complexed with estrone and NAD
Components17-beta-hydroxysteroid dehydrogenase type 1
KeywordsOXIDOREDUCTASE / 17BETA-HSD1 / ESTRONE / FUNCTIONAL ANALYSES / STEROID / NAD/NADH
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 / estrogen metabolic process / NADP+ binding / 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 domain superfamily
Similarity search - Domain/homology
Chem-J3Z / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 17-beta-hydroxysteroid dehydrogenase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
Model details17beta-HSD1-E1 complex
AuthorsLi, T. / Lin, S.X. / Yin, H.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: J.Steroid Biochem.Mol.Biol. / Year: 2023
Title: New insights into the substrate inhibition of human 17 beta-hydroxysteroid dehydrogenase type 1.
Authors: Li, T. / Song, X. / Stephen, P. / Yin, H. / Lin, S.X.
History
DepositionMar 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 17-beta-hydroxysteroid dehydrogenase type 1
B: 17-beta-hydroxysteroid dehydrogenase type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5755
Polymers69,9782
Non-polymers1,5973
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-42 kcal/mol
Surface area21900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.050, 108.150, 117.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 17-beta-hydroxysteroid dehydrogenase type 1 / 17-beta-HSD 1 / 20 alpha-hydroxysteroid dehydrogenase / 20-alpha-HSD / E2DH / Estradiol 17-beta- ...17-beta-HSD 1 / 20 alpha-hydroxysteroid dehydrogenase / 20-alpha-HSD / E2DH / Estradiol 17-beta-dehydrogenase 1 / Placental 17-beta-hydroxysteroid dehydrogenase / Short chain dehydrogenase/reductase family 28C member 1


Mass: 34989.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B1, E17KSR, EDH17B1, EDH17B2, EDHB17, SDR28C1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P14061, 3(or 17)beta-hydroxysteroid dehydrogenase, 17beta-estradiol 17-dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-J3Z / (9beta,13alpha)-3-hydroxyestra-1,3,5(10)-trien-17-one / Estrone


Mass: 270.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 36.82 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: KH2PO4, PEG 8000 / PH range: 7.5-7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.25→25 Å / Num. obs: 26759 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.983 / Rpim(I) all: 0.075 / Rrim(I) all: 0.202 / Net I/σ(I): 7.9 / Num. measured all: 196005
Reflection shellResolution: 2.25→2.37 Å / % possible obs: 100 % / Redundancy: 7.4 % / Num. measured all: 28323 / Num. unique obs: 3824 / CC1/2: 0.932 / Rpim(I) all: 0.185 / Rrim(I) all: 0.509 / Net I/σ(I) obs: 3.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.562
Highest resolutionLowest resolution
Rotation24.99 Å2.53 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
MOSFLM7.2.0data reduction
SCALA3.3.22data scaling
MOLREP11.4.05phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JTV

1jtv


Resolution: 2.25→24.99 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.21 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25465 1382 5.2 %RANDOM
Rwork0.18982 ---
obs0.19316 25322 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.441 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å2-0 Å20 Å2
2---3.81 Å2-0 Å2
3---1.46 Å2
Refinement stepCycle: 1 / Resolution: 2.25→24.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4248 0 58 77 4383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124404
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164129
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.6445987
X-RAY DIFFRACTIONr_angle_other_deg0.5071.5569584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.685556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.548544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.0410719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0670.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025053
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02877
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5463.8072224
X-RAY DIFFRACTIONr_mcbond_other3.5463.8062223
X-RAY DIFFRACTIONr_mcangle_it5.1625.692774
X-RAY DIFFRACTIONr_mcangle_other5.1635.6912775
X-RAY DIFFRACTIONr_scbond_it4.4174.5152180
X-RAY DIFFRACTIONr_scbond_other4.4164.5162181
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6616.5553212
X-RAY DIFFRACTIONr_long_range_B_refined8.6851.2354813
X-RAY DIFFRACTIONr_long_range_B_other8.67951.2344814
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 95 -
Rwork0.277 1828 -
obs--100 %

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