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- PDB-1jtv: Crystal structure of 17beta-Hydroxysteroid Dehydrogenase Type 1 c... -

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Basic information

Entry
Database: PDB / ID: 1jtv
TitleCrystal structure of 17beta-Hydroxysteroid Dehydrogenase Type 1 complexed with Testosterone
Components17 beta-hydroxysteroid dehydrogenase type 1
KeywordsOXIDOREDUCTASE / steroid hormones / alternative binding mode
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
TESTOSTERONE / 17-beta-hydroxysteroid dehydrogenase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.54 Å
AuthorsShi, R. / Nahoum, V. / Lin, S.X.
CitationJournal: FASEB J. / Year: 2003
Title: Pseudo-symmetry of C19 steroids, alternative binding orientations, and multispecificity in human estrogenic 17beta-hydroxysteroid dehydrogenase.
Authors: Gangloff, A. / Shi, R. / Nahoum, V. / Lin, S.X.
History
DepositionAug 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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: 17 beta-hydroxysteroid dehydrogenase type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2683
Polymers34,8881
Non-polymers3812
Water4,053225
1
A: 17 beta-hydroxysteroid dehydrogenase type 1
hetero molecules

A: 17 beta-hydroxysteroid dehydrogenase type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5376
Polymers69,7762
Non-polymers7614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7170 Å2
ΔGint-40 kcal/mol
Surface area21720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.369, 43.944, 60.614
Angle α, β, γ (deg.)90.00, 99.24, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the two fold crystallographic axis

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Components

#1: Protein 17 beta-hydroxysteroid dehydrogenase type 1 / 20 alpha-hydroxysteroid dehydrogenase


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-TES / TESTOSTERONE


Mass: 288.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28O2
#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.: 225 / 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: 46.61 %
Crystal growTemperature: 300 K / pH: 7.5
Details: PEG 4000,magnesium chloride,beta-octylglucoside,glycerol,Hepes,soaking with testosterone, pH 7.5, temperature 300K
Crystal grow
*PLUS
Temperature: 27 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
117 mg/mlprotein1drop
240 mMTris1droppH7.5
31 mMEDTA1drop
40.2 mMdithiothreitol1drop
520 %glycerol1drop
60.06 %(w/v)beta-octylglucoside1drop
730 %PEG40001reservoir
80.16 M1reservoirMgCl2
9100 mMHEPES1reservoirpH7.5
1020 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.54→40 Å / Num. all: 148865 / Num. obs: 46122 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 19.1
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2 / Num. unique all: 4586 / % possible all: 99.4
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 148865
Reflection shell
*PLUS
% possible obs: 99.4 % / Num. unique obs: 4586 / Num. measured obs: 13768 / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1IOL

1iol


Resolution: 1.54→13.9 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2333 -RANDOM
Rwork0.196 ---
all-46084 --
obs-43751 95 %-
Displacement parametersBiso mean: 26.4 Å2
Refinement stepCycle: LAST / Resolution: 1.54→13.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2124 0 27 225 2376
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d1.4
Refinement
*PLUS
Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.54 Å / Lowest resolution: 1.6 Å / Rfactor Rfree: 0.297 / Rfactor Rwork: 0.284

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