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- PDB-1a27: HUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 C-TERMINAL DELE... -

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Basic information

Entry
Database: PDB / ID: 1a27
TitleHUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 C-TERMINAL DELETION MUTANT COMPLEXED WITH ESTRADIOL AND NADP+
Components17-BETA-HYDROXYSTEROID-DEHYDROGENASE
KeywordsDEHYDROGENASE / 17-BETA-HYDROXYSTEROID / MUTANT / ESTRADIOL / NADP
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
ESTRADIOL / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 17-beta-hydroxysteroid dehydrogenase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMazza, C. / Breton, R. / Housset, D. / Fontecilla-Camps, J.-C.
Citation
Journal: Thesis, Universite Joseph Fourier / Year: 1997
Title: Human Type I 17Beta-Hydroxysteroid Dehydrogenase: Site Directed Mutagenesis and X-Ray Crystallography Structure-Function Analysis
Authors: Mazza, C.
#1: Journal: J.Biol.Chem. / Year: 1998
Title: Unusual Charge Stabilization of Nadp+ in 17Beta-Hydroxysteroid Dehydrogenase
Authors: Mazza, C. / Breton, R. / Housset, D. / Fontecilla-Camps, J.C.
#2: 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.
#3: 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
DepositionJan 16, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_residues / Item: _diffrn_source.type
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Aug 2, 2023Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues / 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
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)32,4893
Polymers31,4731
Non-polymers1,0162
Water2,828157
1
A: 17-BETA-HYDROXYSTEROID-DEHYDROGENASE
hetero molecules

A: 17-BETA-HYDROXYSTEROID-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9786
Polymers62,9472
Non-polymers2,0324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9140 Å2
ΔGint-47 kcal/mol
Surface area21150 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)111.380, 48.540, 60.770
Angle α, β, γ (deg.)90.00, 115.13, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 17-BETA-HYDROXYSTEROID-DEHYDROGENASE


Mass: 31473.318 Da / Num. of mol.: 1 / Mutation: C-TERMINAL DELETION (290 - 327)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: SPODOPTERA FRUGIPERDA / Cellular location: CYTOPLASM / Plasmid: PVL1393 / Cell line (production host): SPODOPTERA FRUGIPERDA / Cellular location (production host): CYTOPLASM / 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
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


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


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.13 Å3/Da / Density % sol: 42 %
Crystal growpH: 7.1
Details: PROTEIN WAS CRYSTALLIZED FROM 12-16 % PEG4000, 100 MM HEPES PH 7.1, 0.5 MM ESTRADIOL, 200 MM NACL, 100MM MGCL2, 2.2 MM DECYL-BETA-D-MALTOSIDE; THEN SOAKED IN 30 % PEG 4000, 100 MM HEPES PH 7. ...Details: PROTEIN WAS CRYSTALLIZED FROM 12-16 % PEG4000, 100 MM HEPES PH 7.1, 0.5 MM ESTRADIOL, 200 MM NACL, 100MM MGCL2, 2.2 MM DECYL-BETA-D-MALTOSIDE; THEN SOAKED IN 30 % PEG 4000, 100 MM HEPES PH 7.1, 100 MM MGCL2, 0.5 MM ESTRADIOL, 1 MM NADP+

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.9827
DetectorType: ESRF / Detector: CCD / Date: Feb 1, 1996 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9827 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 15988 / % possible obs: 70.6 % / Observed criterion σ(I): 0 / Redundancy: 2.83 % / Rsym value: 0.034
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.12 % / Rsym value: 0.162 / % possible all: 34.5

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FDT

1fdt


Resolution: 1.9→10 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.261 805 5 %RANDOM
Rwork0.21 ---
obs-15081 --
Displacement parametersBiso mean: 32.83 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 68 157 2406
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.030.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.4591.5
X-RAY DIFFRACTIONp_mcangle_it2.3093
X-RAY DIFFRACTIONp_scbond_it2.6252
X-RAY DIFFRACTIONp_scangle_it4.0084
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.1940.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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